Ordered Assembly of Multiple DNA Fragments

ABSTRACT

A composition and its uses and additionally a kit are provided. The composition is a synthetic self-complementary oligonucleotide that has a double-stranded region and a loop, wherein the double-stranded region contains a binding sequence for PaqCl. Additionally, the oligonucleotide includes unligatable 3′ and 5′ ends that cannot be cleaved by PaqCl. This oligonucleotide composition has been combined with PaqCl or a variant of PaqCl Type IIS restriction endonuclease in a reaction mixture, where the reaction mixture includes PaqCl or variant that can further be combined with a ligase and optionally a deadenylase, crowding molecule such as PEG and/or a repair enzyme such as Endo MS. The kit includes the oligonucleotide and Type IIS restriction endonuclease in the same or different containers.

CROSS REFERENCE

This application is a continuation-in-part of U.S. application Ser. No. 17/286,066 filed Apr. 16, 2021. This application also claims the benefit of U.S. Provisional Application No. 63/125,530, filed Dec. 15, 2020; U.S. Provisional Application No. 63/213,807, filed Jun. 23, 2021; and U.S. Provisional Application No. 63/213,859, filed Jun. 23, 2021. The contents of these applications are incorporated herein by reference in their entirety.

BACKGROUND

Assembly of large DNA molecules from smaller component DNA molecules is an important feature of synthetic biology. A variety of methods have been developed that include sequence and ligation-independent cloning (SLIC) (Li et al. Nat. Methods Res vol 4, 251-256 (2007)), Golden Gate (Engler et al. PLOS one 3, e3647 (2007), Engler et al. PlosOne e5553 (2009)), circular polymerase extension cloning (CPEG) (Quan et al. PlosOne 4, e 6441(2009)), NEBuilder® (New England Biolabs, Ipswich, Mass.), seamless ligation cloning extract (SLICE) (Zhang et al. NAR 40, e55 (2012) and ordered gene assembly in Bacillus subtilis (OGAB) (Tsuge et al. Scientific Reports, 5, 10655 (2015)). These methods vary with respect to in vitro and in vivo assembly methods, homologous recombination approaches and various uses of exonucleases and ligases. The success of any assembly method is dependent on yield, efficiency and fidelity of assembled fragments, yet there has been very little systematic analysis of the criteria on which these parameters depend. In the method referred to as Golden Gate assembly, fragments of DNA are created using restriction endonucleases that generate single strand overhangs on double stranded DNA. Ligation then occurs between overhangs on different fragments to assemble a single double stranded molecule from the fragments. It would be desirable to identify preferred overhangs for polynucleotide fragment assembly under specified criteria for a desired number of fragments and to collate these with other factors and conditions that permit large numbers of fragments to be faithfully assembled in a desired order and a practical amount in a time efficient manner.

One aspect of Golden Gate assembly methods is its reliance on a Type IIS restriction endonuclease and a ligase (Smolke Nat. Biotechnol. 27: 1099-1102 (2009); Engler et al. PlosOne e5553 (2009); Engler et al. Methods Mol. Biol., 729:167481 (2011); Marillonnet et al. Methods Mol. Biol. 1321: 269-284 (2015)). The ligase of choice is generally a T4 DNA ligase (New England Biolabs, Ipswich, Mass.).

Like many or most enzymes, T4 DNA ligase has a bias with respect to ligating various complementary overhangs. Moreover, the use of T4 DNA ligase was described for joining mismatches, gaps and other imperfect structures with varying levels of efficiency (Potapov et al. ACS Synthetic Biology, 7, 2665-2674 (2018); Nilsson et al, Nucleic Acids Res. 10:1425-1437 (1982); Goffin et al. Nucleic Acids Res. 15:8755-8771 (1987); Wu et al, Gene, 76: 245-254 (1989); Harada et al, Nucleic Acids Res., 21, 2287-2291 (1993); Showalter et al. Chem Rev. 106: 340-360 (2006); Engler et al. PlosOne e5553 (2009); Engler et al. Methods Mol. Biol., 729:167-181 (2011); Engler et al. Methods Mol. Biol., 1116, 119-131 (2014)).

There have been some initial attempts to identify, using a computer and instructions, suitable overhangs for a selected number of fragments (see for example, MoClo, Golden Braid, Mobius Assembly, MIDAS). These computer-based overhang selection methods restrict the user to a limited number of 4-base overhangs, which is particularly constraining when sequences may not be chosen arbitrarily (e.g., when assemblies must break within coding sequences). These restrictions extend to relatively small, standardized sets of overhangs. The number of fragments that can be assembled has been limited by the number of allowable overhang pairs, typically limiting the user to 6-8 fragments at a time (GeneArt, TherrnoFisher, Waltham, Mass.). Successive hierarchical assembly rounds of 6-8 fragments are then required to build large DNA constructs. It would be desirable to be able to join many more than 6-8 fragments in a single reaction to more rapidly build large DNA molecules. However, increased numbers of fragments enhance experimental complexity arising from not only the biochemical conditions required for accurate and efficient assembly but also the computer tools that would be desirable for identifying the best set of fragment ends to enable large numbers of fragments to be assembled. For example, increasing the number of fragments in an assembly reaction has the effect that each successive fragment adds two new overhangs into the ligation (i.e., an overhang in the fragment and a complementary overhang in the next fragment in the assembly). Since different overhangs ligate with different fidelities under different conditions, the addition of one more fragment that have an overhang that can promiscuously ligate to one or more of the other overhangs under the ligation conditions used can drastically decrease the overall yield of the ligation. This problem is exacerbated by the fact that in some cases a user may wish to avoid using certain overhangs or may be restricted to overhangs only found in a particular window in a sequence. Thus, for higher order assembly reactions, (e.g., reactions in which at least 8 fragments are ligated together) and assembly reactions that require ligations to occur at or near a particular site, standardized sets of overhangs are of limited use. It would be desirable to have a computer aided resource that enables the user to quickly identify a preferred set of overhangs for any number of overhangs based on biochemical data for any and all combination of overhangs of a selected length. Given certain limitations imposed by the standard enzymes used in the standard Golden Gate assembly method, it would also be desirable to optimize other experimental conditions associated with enzyme function for high fidelity assembly and to correlate these optimizations with the selection of a preferred set of overhangs selected by the computer.

SUMMARY

Methods are provided for forming a target polynucleotide from an ordered set of double stranded polynucleotide fragments, that include (a) determining for the target polynucleotide, an optimized overhang sequence for each polynucleotide fragment for joining into an ordered set to assemble the target polynucleotide. Each overhang sequence corresponds to a plurality of nucleotides wherein the overhang sequences have been optimized individually and as a set according to their experimentally determined ligation fidelity scores; and (b) obtaining double stranded polynucleotide fragments by enzyme cleavage of double stranded DNA having the plurality of nucleotides in the overhang corresponding to the optimized overhang sequence.

Examples of the experimental conditions for ligating overhang pairs for polynucleotide fragments assembly may include one or more of the following features:

the enzyme for cleavage of double stranded DNA is a Type IIS restriction endonuclease capable of cleaving a double stranded DNA outside its recognition or binding site to generate a proximate single strand overhang of a length that is specific to a particular endonuclease or its ortholog (see Example 1); (the terms “recognition” and “binding” are used interchangeably throughout).

the cleavage endonuclease has a recognition sequence of at least 5 bases preferably at least 6 bases, preferably at least 7 bases;

the properties of the selected endonuclease is capable of efficiently performing in a reaction that includes a ligase to assemble as many as 24-100 fragments;

the overhang selected is a DNA of 2, 3, 4 or 5 nucleotides in length;

the set of polynucleotide fragments contains at least 2 fragments, at least 5 fragments, at least 10 fragments, at least 15 fragments, at least 20 fragments or at least 50 fragments, at least 60 fragments or as many as 100 fragments;

the ligase is a DNA ligase such as T4 DNA ligase or variant thereof such as a thermostable variant or high salt tolerant ligase;

the target nucleic acid may include pieces of nucleic acid from different genomes to form a molecule that has no counterpart in nature. Alternatively, virus genomes, bacterial genomes and chromosomes may be assembled using the methods described herein. Individual genes, operons and metabolic pathways may be similarly constructed;

the polynucleotide fragments can be made enzymatically from nucleotides or by chemical synthesis once an optimal set of overhangs have been identified;

the polynucleotide fragments for use in assembly may be amplicons or are clonal inserts. Multiplex amplification of an entire set of polynucleotide fragments in a single reaction vessel makes a streamlined protocol for target polynucleotide assembly in the presence of a ligase and a Type IIS restriction endonuclease;

multiplex amplification of all the fragments in a particular assembly reaction may be performed in the same reaction tube where once the polymerase has been inactivated, the ligase and restriction endonuclease may be added to cause the ordered assembly of fragments;

temperature cycling for endonuclease cleavage and ligation may vary between touch-down, touch-up and drop-down cycling. The cycling conditions may vary from a high temperature of 37° C.-50° C. down to 16° C. However, the range may be broader depending on the ligase and restriction endonuclease used. The salt concentration of the reaction buffer may also vary to include 100 mm salt; and

a reaction mixture comprising a DNA ligase, a restriction endonuclease and a plurality of double stranded nucleic acid fragments having single strand overhangs at the 5′ or 3′ ends suitable for high fidelity ligation in a predetermined order where various overhangs of a selected length (2-base, 3-base, 4-base or 5-base) are described in Table 3, Table 4, Table 5 or Table 6.

In one aspect, a kit is provided that includes a phage derived ligase and a bacterial Type IIS restriction endonuclease combined in a single buffer and a destination vector with instructions for use.

The above experimental conditions assist a user in generating target polynucleotides from fragments. These experimental conditions may be combined with the computer analyses described below that generate optimal sets of overhang sequences and/or identify fragment lengths for synthesis of polynucleotide fragments to accurately and efficiently construct target polynucleotides from target polynucleotide sequences in sequence databases.

Another example provides a method that enables a user to generate a target nucleic acid molecule, where the method includes: (a) receiving into a computer a target nucleic acid sequence corresponding to the target double strand nucleic acid molecule; (b) providing access to a database that includes ligation frequency data for a set of overhang sequences having a defined length; (c) using the database to generate a set of n polynucleotide sequences that when combined, form the target nucleic acid sequence, each polynucleotide sequence having a first end and a second end, such that the first and the second end have different non complementary overhang sequences selected from the set of overhang sequences; wherein: (i) every overhang sequence in a set of overhang sequences is different; (ii) the selection of overhangs is based on ligation fidelity obtained from the database of each member of the set of overhang sequences; (iii) the overhang sequence at a first end of a first polynucleotide is complementary to an overhang sequence at the first end of a second polynucleotide to permit hybridization and ligation for ordered joining of the first and second polynucleotide; (iv) each fragment sequence of the set of n polynucleotide sequences corresponds to a different portion of the target nucleotide sequence; (d) outputting a set of n polynucleotides sequences in a user accessible medium; and (e) enabling the user to construct the target nucleic acid molecule from a plurality of polynucleotide molecule fragments, wherein for each polynucleotide sequence of the set of n polynucleotide sequences; generating an overhang on the polynucleotide fragment corresponding to a selected overhang sequence from the set of overhangs having an overall preferred ligation fidelity score for ordered assembly of the polynucleotides by hybridizing and ligating the overhangs.

Various embodiments include one or more of the following features: the set of n polynucleotide sequences comprises n−1 oligonucleotide sequence pairs suitable for hybridization, each polynucleotide sequence terminating at a first end with a first overhang sequence and respectively terminating at a second end with a second and a third overhang sequence; and a set of overhangs comprise a sequence of at least 2 nucleotides; wherein the sequences for each of the first and second overhangs on each polynucleotide are optimized.

In one example, a method is provided that includes: providing a user interface on a computer system that enables a user of the computer system to: enter into the computer system: a set of unique 5′→3′ 2-base, 3-base, 4-base or 5-base overhangs; and experimental conditions for ligation of a set of polynucleotide fragments, each fragment of the set of fragments terminating in a different one of the set of overhangs; and receive output from the computer system, the output comprising an estimated overall ligation fidelity score for the entered set of overhangs under the entered experimental conditions, wherein the computer system automatically generates and outputs the overall ligation fidelity for the entered set of overhangs under the entered experimental conditions by: accessing a database comprising experimentally determined ligation fidelity for 2, 3, 4 or 5-base overhangs; retrieving from the database, a ligation frequency score for the entered overhang set; and deriving the estimated overall ligation frequency score from the retrieved ligation frequency for each overhang in the entered 3 or 4-base overhang set from the database.

Various embodiments include one or more of the following features: the received output from the computer system provides estimated frequencies of ligation events for non-Watson-Crick overhang pairs of the input set of overhangs; the estimated frequencies of ligation events for non-Watson-Crick overhang pairs of the input set of overhangs are represented graphically in a two-dimensional array in which a given array element includes a graphical indication of an estimated frequency of ligation events for an overhang corresponding to an array row of the given element with an overhang corresponding to an array column of the given element; the user interface on the computer system is implemented within a browser and wherein the computer system accesses the database via a wide area network; and the database is hosted in the cloud.

Additionally, the computer system may have: a memory for storing computer-readable instructions; and a processor connected to the memory, wherein the processor, when executing the computer-readable instructions, causes the system to perform a method comprising: providing a user interface on the system that enables a user of the system to: enter into the system: a set of unique 2, 3, 4 or 5-base overhangs; and experimental conditions for ligation of a set of polynucleotide fragments, each fragment of the set of fragments terminating in a different one of the set of overhangs; and receive output from the system, the output comprising an estimated overall ligation fidelity for the entered set of overhangs under the entered experimental conditions, wherein the system automatically generates and outputs the overall ligation fidelity for the entered set of overhangs under the entered experimental conditions by: accessing a database comprising experimentally determined ligation fidelity for 2, 3, 4 or 5-base overhangs; retrieving from the database ligation fidelity for the entered overhang set; and deriving the estimated overall ligation fidelity by averaging the retrieved ligation fidelity retrieved from the database over the entered 3 or 4-base overhang set.

In another aspect, a computer program product is provided with the following features: a non-transitory computer-readable medium with computer program instructions encoded thereon, wherein the computer program instructions, when processed by a computer system, instruct the computer system to perform a method comprising: providing a user interface on the computer system that enables a user of the computer system to: enter into the computer system: a set of unique 5′ 4 3′ 3 and/or 4-base overhangs; and experimental conditions for ligation of a set of oligonucleotide fragments, each fragment of the set of fragments terminating in a different one of the set of overhangs; and receive output from the computer system, the output comprising an estimated overall ligation fidelity for the entered set of overhangs under the entered experimental conditions, wherein the computer system automatically generates and outputs the overall ligation fidelity for the entered set of overhangs under the entered experimental conditions by: accessing a database comprising experimentally determined ligation fidelity and hybridization fidelities for 4-base canonical ACGT overhangs; retrieving from the database ligation fidelity and hybridization fidelities for the entered overhang set; and deriving the estimated overall ligation fidelity by averaging the retrieved ligation fidelity and hybridization fidelities retrieved from the database over the entered 4-base overhang set.

In another aspect, a method is provided for forming a target nucleic acid from an ordered set of polynucleotides, that includes: (a) a computer system receiving from a user a sequence for the target nucleic acid; and (b) generating polynucleotide sequences suitable for ordered assembly of the target nucleic acid by hybridization and ligation of 2, 3, 4 or 5-base overhang pairs, wherein an overhang is positioned at a terminus of a first polynucleotide in the set of polynucleotides, and the complement of overhang is positioned at the terminus of a second polynucleotide selected for forming a junction between the two polynucleotides in the set of polynucleotides.

In one embodiment, the junction sequence between the two polynucleotides have been optimized separately and as a set according to ligation parameters of oligonucleotide molecules obtained from a database.

In another embodiment, a computer-generated report to any composition or method described above is provided that contains one or more of the following: primers to be ordered; assembly sequence file with or without annotation; annotated assembly sequence file containing target DNA inserts, overhangs, and/or a vector backbone; a graphic of assembled construct; and/or a downloadable pdf formatted assembly graphic.

In one example, a composition is provided that includes a system hosting a target polynucleotide assembly application with a display, wherein the system is in data communication with a server hosting software for fragment editing, displaying a graphical user interface for collaborative or individual editing of a gene synthesis project, the graphical user interface comprising: a representation of a target nucleic acid molecule built from component parts wherein the sequence of the target nucleic molecule is entered by the user; the system determining the component parts for joining at junction regions wherein the junction regions achieve predetermined hybridization parameters determined for each junction region and for the sum of the junction regions; wherein the system further comprises one or more links selected from the group consisting of links to: sequence databases; protein structure databases; functional features of selected sequences; hybridization efficiency databases; source enzymes for the gene synthesis project; and change notes entered by one or more editors collaborating to edit the gene synthesis project.

In another example, a computer implemented method is provided for selecting a set of overhangs for an assembly reaction to be performed under selected experimental conditions, that includes:

-   -   (a) receiving: (i) a desired number of overhangs for an assembly         reaction and (ii) a length of the overhangs;     -   (b) selecting a set of overhangs from an overhang table wherein         in one example, the overhang table contains all possible         overhangs, and wherein the overhangs in the table are of the         length received in (a) and wherein the selected set of overhangs         has the desired number of overhangs;     -   (c) for each individual overhang in the set, calculating a         ligation fidelity score, wherein the ligation fidelity score of         each individual overhang represents the frequency at which the         individual overhang and its complement independently ligate to a         perfectly complementary overhang relative to all overhangs in         the set and their complements;     -   (d) calculating an overall fidelity score for the set of         overhangs based on the calculated ligation fidelity scores for         each of the individual overhangs, as output in step (c);     -   (e) iterating steps (b)-(d) until a plurality of overall         fidelity scores have been calculated, each for a different set         of overhangs; and     -   (f) identifying the set of overhangs that has a suitable overall         fidelity score.

In examples of the method, other features may be selected for use in the computer implementation. These features may include one or more of the following:

-   -   1) selecting overhangs in (b) with the features that each of the         overhangs is unique within the set, is not complementary to         another overhang in the set, and is not palindromic;     -   2) calculating the fidelity score in step (c) further comprises         consulting the ligation frequency table comprising individual         experimentally-defined measurements of the number of ligation         events;     -   3) calculating the ligation fidelity score in (c) for an         individual overhang from the number of ligation events that         occur between the individual overhang and its complement         relative to the total number of ligation events that occur         between i. the individual overhang and all of the overhangs in         the set and their complements and ii. the complement of the         individual overhang and all of the overhangs in the set and         their complements;     -   4) receiving in step (a): (iii) overhangs that should be         excluded, and wherein the overhangs selected in step (b) do not         include the excluded overhangs;     -   5) receiving in step (a): (iii) ligation conditions, for         example, one or more of a ligase, a salt concentration, a         temperature, temperature range and/or thermocycling conditions         for cleavage and ligation; and wherein in step (c) the         calculated overall fidelity scores are for ligations done in the         specified ligation conditions;     -   6) multiplying the ligation fidelity scores for each individual         overhang calculated in step (c) to calculating the overall         fidelity score in (d);     -   7) receiving: (iii) a nucleotide sequence of an assembly         and (iv) a set of intervals in which the nucleotide sequence         of (iii) can be cleaved; and between steps (a) and (b)         identifying a non-redundant set of sub-sequences in the         intervals that are the same length as the overhang length input         in (a)(ii) and storing the non-redundant set of sub-sequences as         the overhang table of step (b).         -   Further specifics for (7) may include:         -   splitting the nucleotide sequence of the assembly at             overhangs identified in (f), thereby producing a set of             fragments of the assembly, where the ends of the fragments             are defined by the identified overhangs;         -   defining each interval of (iv) by beginning and end             coordinates in the nucleotide sequence of the assembly.     -   8) In step (a) receiving the length of 4 for the overhang length         and wherein optionally the overhang table of (b) has 256         overhangs;     -   9) In step (a) receiving the length of 3 for the overhang length         and wherein optionally the overhang table of (b) has 64         overhangs;     -   10) In step (e) iterating steps (b)-(d) at least 1000 times.         -   Additional features of the computer implemented method may             include:         -   inputting into an interface: (i) the desired number of             overhangs for an assembly reaction, (ii) the length of the             overhangs; optionally, (iii) the nucleotide sequence of the             assembly (iv) the set of intervals in which the nucleotide             sequence of (iii) can be cleaved;         -   causing the computer implemented method described above to             be executed; and         -   receiving a set of overhangs as identified in step (f)             and/or if (iii) and (iv) are input, then receiving a set of             fragments of the assembly, where the ends of the fragments             are defined by the overhangs identified in step (f).

In one example of the above additional features includes: receiving the ligation conditions for ligating the set of overhangs or fragments containing the same, and, optionally, thermocycling conditions for producing the fragments and ligating them together. Another example includes making a set of double stranded nucleic acids that have a set of overhangs that have the highest overall fidelity score, and their complements. Another example includes: ligating the fragments together in a single reaction to produce an assembly, wherein in the reaction the overhangs determine the order of the fragments in the assembly. Another example includes performing ligation by overhang-directed ligation.

Additional features of the computer implemented method may include: receiving in step (a): (iii) a nucleotide sequence of an assembly (iv) a set of intervals in which the nucleotide sequence of (iii) can be cleaved; and between steps (a) and (b) the method comprises: identifying a non-redundant set of sub-sequences in the intervals that are the same length as the overhang length input in (a)(ii) and storing the non-redundant set of sub-sequences as the overhang table of step (b). In one example of the additional features, step (a) further includes receiving experimental conditions for cleavage.

Additional features of the computer implemented method includes a computer-readable medium comprising programming for performing any of the above described features and examples of the method.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1A-1B shows Golden Gate assembly in which a restriction endonuclease enzyme generates an overhang by cleaving the polynucleotide at a sequence adjacent to the restriction endonuclease recognition (or binding) site resulting in 5′ overhangs (NNNN).

FIG. 1A shows a fragment that contains the desired recognition sequence of the chosen restriction endonuclease (here GGTCTC (Bsal-HF®v2, New England Biolabs, Ipswich, Mass.)) and a desired overhang sequence (NNNN) resulting from enzyme cleavage on either side of a polynucleotide fragment insert. The recognition and overhang sequences may be introduced during synthesis of the desired DNA fragment by, for example, chemical synthesis; in primers used for DNA amplification; or in a vector at a site into which the polynucleotide fragment is inserted.

FIG. 1B shows how ten polynucleotide fragments (A-J) can be joined through overhang pairs formed by restriction endonuclease cleavage in FIG. 1A from 9 junctions. “End junctions” enable joining of the target nucleic acid to each end of a master plasmid. The 5′ 4-base overhang on one polynucleotide fragment can hybridize with the complementary overhang on a second polynucleotide fragment. Ligation of the hybridized overhangs forms a junction. Providing each junction sequence is unique, multiple fragments are capable of alignment in a unique ordered manner.

FIG. 2A-2C shows one view of a fragment assembly reaction design. In this view, 12 polynucleotides that have been obtained either by genetic engineering of DNA molecules (for example, genomic DNA) or by chemical synthesis (short fragments typically less than 500 base pair (bp)) or by amplification (varied length fragments typically less than 2 kb) for assembly into a target nucleic acid. In this way, a sequence or set of sequences described in one or more database or other recorded means can be translated into the assembled target nucleic acid in a test tube.

FIG. 2A shows 12 fragments each integrated into individual “donor” plasmids which may be the same or different from each other.

FIG. 2B shows a destination vector and enzymes required for assembly. In this example, the enzymes are T4 DNA ligase and a Type IIS restriction endonuclease (Bsal-HFv2).

FIG. 2C shows how the 12 fragments are then cleaved from the donor plasmids (using Bsal-HFv2), joined in order and integrated by means of a T4 DNA ligase into a master plasmid containing the antibiotic resistance gene. The assembly is seamless, cell free, does not require PCR, and is amenable to standardization and automation.

FIG. 3A-3C shows high efficiency of generation of bacterial clones obtained on antibiotic plates from destination plasmids containing 12 fragments as shown in FIG. 2A-2C. The efficiency is shown to match predictions. The assembly is performed in a single reaction vessel, with choice of junctions driven by the ligation fidelity and bias profiling. Plates shown are representative replicates, with a white filter (top) to show blue colonies expressing β-gal, and a black filter (bottom) to visualize white colonies containing antibiotic resistance but a non-functional lac cassette.

FIG. 3A shows the results of a designed predicted high fidelity 12-fragment set, predicted 99% blue colonies, observed average over 8 replicates, 99.2±0.6%.

FIG. 3B shows results of the designed low fidelity, deletion-prone 12-fragment set; predicted 31% blue colonies, observed average of 8 replicates, 45±5%.

FIG. 3C shows the results of assembly of the designed 24-fragment high fidelity set, predicted 91% blue colonies, observed average over 10 replicates, 84±5%.

FIG. 4A-4B shows how sequences of polynucleotides can be identified from databases and designed to form novel gene constructs in modular assembly. Sequence components from different sources (different species) can be identified and assembled to form a novel target nucleic acid.

FIG. 4A shows sets of promoters, ribosome binding sites, genes and terminators. The user selects single sequences in each category to design a gene expression unit.

FIG. 4B shows a second assembly design where a gene is constructed from multiple components. Each newly assembled gene has a different promoter sequence and also varies in the type of terminator sequence.

FIG. 5A-5B shows that ligation yields vary according to the composition of overhangs for defined substrates. Ligation yield is measured against ligation time courses for defined substrates having 3-base overhangs. These values contribute to an assessment of ligation efficiency. The 3′-end of the phosphorylated strand was FAM labeled. Ligation reactions were composed of 1×T4 DNA ligase reaction buffer, 350 nM T4 DNA ligase and 100 nM FAM-labeled DNA substrate and 100 nM polynucleotides with a range of overhangs where ligation was measured by scarless joining of two polynucleotides with complementary overhangs (overhang pairs). Reactions were performed at 25° C., with incubation time points from 0 to 30 minutes. Reported values are the average of a minimum of 3 replicates with the error bars showing the standard deviation.

FIG. 5A shows ligation yields over time obtained using a polynucleotide with an ANT overhang pair versus a TNA overhang pair showing that ligation yield with ANT was significantly higher than with TNA. This suggests that TNA overhangs should be avoided.

FIG. 5B shows ligation yields over time obtained using a polynucleotide with a 5′GGC/3′TCG overhang pair versus a 5′TCG/3′ GGC overhang pair showing that the ligation yield was significantly higher for GGC/TCG than for TCG/GGC. This shows that orientation of the overhangs is a parameter that should be considered in selecting overhangs for ordered fragment assembly.

FIG. 6A-6D show that overhangs with different sequences have varying frequency of specific base pair mismatches by position that contributes to a measure of ligase fidelity. The incidence of each possible mismatched base pair observed for ligation of 3 and 4-base overhangs was recorded. The results shown are for Single-Molecule Real-Time (SMRT) sequencing (Pacific Biosciences, Menlo Park, Calif.) of ligation reactions with 100 nM of the multiplexed 3-base overhang polynucleotide. The reactions were performed at various temperatures and for various times as specified for 1.75 μM T4 DNA ligase in standard ligation buffer. Mismatch frequency varies between almost 4% to 0.01% or less.

FIG. 6A shows the mismatch frequency when positions 1 and 3 (N1:N3′) in the 3-base overhang were mismatched for a ligation reaction for 1 hour at 25° C.

FIG. 6B shows the mismatch frequency when position 2 (N2:N2′) in the 3-base overhang were mismatched for a ligation reaction for 1 hour at 25° C.

FIG. 6C shows the mismatch frequency when positions 1 and 3 (N1:N3′) in the 3-base overhang were mismatched for a ligation reaction for 1 hour at 37° C.

FIG. 6D shows the mismatch frequency when position 2 (N2:N2′) in the 3-base overhang were mismatched for a ligation reaction for 1 hour at 37° C.

FIG. 6E shows the mismatch frequency when position 2 and 3 (N2:N3′) in the 4-base overhang were mismatched for a ligation reaction for 18 hours at 25° C.

FIG. 6F shows the mismatch frequency when position 1 and 4 (N1:N4′) in the 4-base overhang were mismatched for a ligation reaction for 18 hours at 25° C.

FIG. 7A-7F provides comprehensive data on ligation efficiency for different randomized 3-base overhangs by T4 DNA ligase and for 4-base overhangs under different reaction times and temperatures. SMRT sequencing results are presented for ligation of 100 nM of the multiplexed 3-base and 4-base overhang substrate for the specified incubation time and temperature, using 1.75 μM T4 DNA ligase in standard ligation buffer. Observations have been normalized to 100,000 ligation events. In FIGS. 7B, 7D and 7F, fully Watson-Crick paired ligation results are below the horizontal line in each histogram and ligation products containing one or more mismatches are above the horizontal line.

FIG. 7A shows the frequency heat map of all ligation events (log-scaled). Three-base overhangs are listed alphabetically left to right (AAA, AAC, AAG . . . TTG, TTT) and bottom to top such that the Watson-Crick pairings are shown on the diagonal.

FIG. 7B shows a stacked bar plot showing the frequency of ligation products containing each overhang, corresponding to each column in the heat map in FIG. 7A.

FIG. 7C and FIG. 7D are similar to FIG. 7A-7B except the experimental conditions are 1 hour at 37° C.

FIG. 7E and FIG. 7F shows assay results for the ligation of randomized 4-base overhangs.

FIG. 7G-7J shows that overhang sequences may be clustered into groups identified as High-fidelity (HF), Low-fidelity (LF), and also Deletion prone (DP) and Failure Prone (FP) (described in Table 1). This data can be used to determine a set of overhangs for a set of fragments to achieve a desired purpose, e.g., optimally efficient joining for efficient assembly or inaccurate joining or evolution studies. The predicted and actual results of joining 10 fragments are provided following identification of a HF set (G) and (I) or LF set (H) and (J) of overhangs under specified conditions of temperature and time. Junction overhangs can be found in Table 1. The intensity of the color corresponds to the number of instances of that junction observed in a SMRT sequencing experiment, normalized to 100,000 total junctions. Predicted frequencies of junctions are based on the fidelity library data generated for the 4-base overhang substrate ligated with T4 DNA ligase at 25° C. for 18 hours. The experimental observations shown are for assembly of the 10-fragment HF and LF sets at 37° C. for 5 minutes and 16° C. for 5 minutes, 30 cycles. The sequences chosen for the junction differ amongst the HF, LF, DP and FP sets, as indicated in Table 1.

FIG. 8 shows, by means of a high-level block diagram, a system for generating an estimated overall ligation fidelity for a user-specified overhang sequence set; and also, experimental conditions to achieve a desired result The system utilizes client 802 having bidirectional data communication 803 with a server 804 that in turn has access to storage 806 via 808 where 806 includes a database of 4-base 5′-3′ ligation fidelity. This can also be a 2-base, 3-base or 5-base database. Bidirectional data communication 803 may be implemented using a local connector such as a local area network (LAN) or a wide area network. Server 804 may be a dedicated resident server or may be implemented in the cloud. Data storage 806 may be co-loaded with server 804. The user enters data into client 802 which may include a browser interface. In addition to running a browser, client 802 may host a graphical user interface for use to enter sets of 5′-3′ 4-base canonical form of AGCT or other overhang sets or for selecting experimental conditions for ligation.

FIG. 9 shows input and output steps in a high-level flow diagram for execution of an assembly reaction using the system outlined in FIG. 8. user enters a set of overhang sequences of any desired length, for example, the set of overhang sequences will be a set of 5′-3′ 4-base overhang sequences 902. The set will contain more than one 4-base overhang sequence such that each member of the set differs from all the other members of the set. Each overhang sequence represents a member of a single overhang pair that the user preferably wishes to use in an experiment to join in order a plurality of double stranded nucleic acid fragments. The 4-base overhang may be represented as a Watson-Crick pair of overhangs. As previously shown (FIG. 5B), a single overhang pair in a set may vary with respect to ligation fidelity depending on whether a particular sequence is a 5′ sequence or its complement. Each member pair is considered separately from the other member pairs in the set. The user may select experimental conditions for ligation of fragments having overhangs corresponding to the entered sequences in 902. These experimental conditions include, for example, time of incubation with ligase and temperature of incubation 904. By accessing a database of ligation fidelity for individual overhangs or overhang pairs, the system generates an output describing the ligation fidelity for the entered overall overhang sequence set and/or for individual overhang pairs in the set 906. The system may additionally output a graphical matrix representation of ligation fidelity for the selected overhang sequence pairs. If the identified fidelity efficiency of the set of 4-base overhang sequences input by the user is rejected by the user, the user is enabled to assess the ligation of the identical set of 4-base overhangs under different selected experimental conditions or to enter a modified set of 4-base overhang sequences under the same or different experimental conditions to determine how to join the set of double stranded nucleic acid fragments in an ordered assembly.

FIG. 10 is a diagrammatic user interface (ViewSet) for inputting a 4-base overhang set and ligase and reaction conditions in the system of FIG. 8. The user inputs a set of 5′-3′ 4-base overhang sequences 1002. The user selects ligation conditions from a drop-down menu 1004; here T4 DNA ligase is selected, and ligation conditions are 18-hour incubation at 25° C. Submission of the information results in the events shown in FIG. 8 and FIG. 9.

FIGS. 11A and 11B are illustrative graphical output displays of the system of FIG. 8-10 showing ligation preferences 1104. The output provides user with an estimated fidelity score meaning the percentage of correctly ligated products 1102. The graphical display can provide as requested by the user, color coded entries for ligation fidelity for overhangs that correspond to good Watson-Crick pairs, poor Watson-Crick pairs, high-count mismatches, modest mismatches and trace mismatches and optionally provides normalized ligation counts. In this figure, a single one-base mismatch is shown in pink. The ligation preferences for all specified overhangs are provided in a tabular format: Overhangs in rows correspond to top strand, Overhangs in columns correspond to bottom strand. Overhangs are written in 5′ to 3′ direction. For example, ATTC overhang in a row and GAAT overhang in a column corresponds to the Watson-Crick pair 5′-ATTC-3′, 3′-TAAG-5′. This is a strongly ligating WC pair as indicated by the dark green color. TACC overhang in a row and GGTT overhang in a column corresponds to a pair 5′-TACC-3′, 3′-TTGG-5 with an A/T mismatch. This is a mismatch ligation that is modestly frequent as indicated by the light grey color.

FIG. 12 is an example of a graphical output of a target nucleic acid in a database for which a corresponding double stranded DNA macromolecule is desired to be synthesized. The computer output provides an optimized map of polynucleotide fragments to be synthesized with the location of joins where the position of joins reflects optimization of an overhang set with specified ligation fidelity across the entire database sequence. Seven fragments (A-G) are shown although there could readily be any number of fragments such as A through Z or as many as 75 or 100 fragments for assembly. An output may include the overhangs for each fragment and primers suitable for amplifying synthetic oligonucleotides by PCR. The primers are optionally input via a computer connection directly into an oligonucleotide synthesis platform for synthesizing DNA primers.

Although FIGS. 7E-7J, and FIGS. 8-12 shows examples of 4-base overhangs, the system may output a set of overhangs with 3-bases or more than 4-bases for the desired overall ligation fidelity for joining the defined number of polynucleotide fragments determined by the user or the system based on the target nucleic acid sequence output. The larger the number of fragments, the more likely that the number of bases in an overhang with be 4 or more.

The overhangs may be input via the client shown in FIG. 8 to generate an output as shown in FIG. 9 where the input set of overhangs may be manually inserted or inserted after computation by the system.

The experimental ligation conditions may be input via the client together with overhangs determined manually or by the system to generate an output as shown in FIG. 9 where the input is manual or inserted after computation by the system that determines the optimal ligation efficiency for a set of overhangs as above.

Under certain circumstances, an optimal ligation efficiency may not be desired so that the user may select a desired fidelity % from a pull-down menu. The system will output polynucleotide sequences, overhang sequences, optionally primer sequences, experimental conditions and a graphical representation of ligation preferences for each member of the set of overhangs (as shown in FIG. 11A-11B).

Ligation efficiency may be determined to be greater for individual overhangs with a single base mismatch than for a Watson-Crick overhang pair. The system output will reflect these preferences to meet the user input for a particular overall ligation fidelity.

The user may select from a drop-down menu, a particular ligase whose properties will affect the choice of overhang pairs and the outputs.

FIG. 13 is a high-level flow diagram showing inputs in addition to system output steps.

Individual examples are provided for user entry of input (1302-1306) generating outputs 1308-1312. However, the input parameters in 1302-1306 may be substituted or added to by any one or more or two or more of the following:

-   -   (a) a target nucleic acid sequence;     -   (b) a set of polynucleotide fragments;     -   (c) a partial set of polynucleotide fragments provided by the         user and a partial set output from the system;     -   (d) a set of vectors having specified junction sequences;     -   (e) a preferred overhang length;     -   (f) excluded overhangs;     -   (g) a set of overhangs of specified length;     -   (h) a partial set of overhangs of specified length provided by         the user and a partial set of overhangs output by the system;     -   (i) a choice of ligase e.g., T4 DNA ligase, T7 DNA ligase, any         other ATP dependent DNA ligase or NAD+ dependent ligase such as         Taq DNA ligase;     -   (j) a choice of restriction endonuclease e.g., one or more of         Esp3l, Sapl, Bbsl-HF; BspQl, Hgal, BsaBl, BsaBl, Bsal,         Bsal-HFv2, Bsil, BsmAl, BsmBl, BsmFl, Bsml, Bsr Dl, Bsrl, BtgZl,         BtsCl, BtsMutl, Btsv2, BspQl, Bpil, Bful, BspMl, Aarl and         isochizomers of the same.     -   (k) a preferred number of fragments;     -   (l) a preferred incubation time; e.g., 1 hour, 5 hours,         overnight;     -   (m) a preferred incubation temperature e.g., 37° C. or 45° C.;     -   (n) preferred reaction conditions in addition to time and         temperature;     -   (o) a preferred overall ligation efficiency;     -   (p) a minimum acceptable ligation efficiency;     -   (q) maximum GC content;     -   (r) maximum AT content;     -   (s) acceptable bias;         -   Output may include one or more of the following:     -   (a) any of the above parameters described above not specified by         the user;     -   (b) warnings if ligation fidelity determined from user input         parameters is too low based on manual input of certain         parameters where the warning might include internal RE sites,         low efficiency junction sites formed from individual overhang         pairs; excessive bias of some ligation events over others;     -   (c) matrix or tabular format for all specified overhang pairs         showing strongly ligating Watson Crick pairs and mismatch         overhang pairs with color coded frequency of occurrence;     -   (d) ligase fidelity viewer grid to show predicted fidelity for         chosen set;     -   (e) provide alternative solutions with altered specified         experimental parameters;     -   (f) graphical display of assembly design, annotated if using         full sequence;     -   (g) exportable fragment/primer sequences for synthesizer.

The system then computes any of the above parameters not provided by the user to achieve the requested output using a database of n-base overhangs and 5′-3′ ligation efficiencies under various reaction parameters to enable the user to create an ordered assembly of X number of fragments with a defined ligation efficiency.

FIG. 14 shows an exemplary interface (GetSet) that is a variation of FIG. 10 for entry of alternative or additional parameters by a user. These include as indicated: overhang length, ligation conditions, number of overhangs in the overhang set, list of overhangs that must be included, excluded overhangs and details of experimental conditions.

FIG. 15 shows output from the FIG. 14 query. Here 10 overhangs are provided (the overhang set) with an estimated ligation fidelity score of 99.8%. The ligation frequency matrix provides ligation frequency values for each overhang pair. The frequency of mismatch ligations for all mismatches is substantially zero.

FIG. 16 shows another interface (SplitSET). Here a DNA sequence for example, a gene, is entered from a database or other source (here 3078 nucleotides). The interface permits the user to request overhang length (4-base), fragment size (here 615 nucleotides) experimental conditions (T4 DNA ligase, incubation 18 hours/25° C.), and numbers of fragments to generate. The user can specify excluded overhangs.

FIG. 17 shows the output from the FIG. 16 query. The output provides a set of fragments with overhangs, an estimated ligation fidelity score with a matrix that shows the frequency of mismatches, the location in the sequence of the overhangs and the fragments for assembly. The fragments may then be ordered from an oligonucleotide synthesis service or by other means.

FIGS. 18A and 18B show assembly efficiency of a Lac cassette from 24 fragments in a single pot using the computer systems described herein to select overhangs (see for example Table 7).

FIG. 18A shows blue colonies from a correctly assembled LacZ cassette. The cassette was assembled from 24 fragments using BsmB1 and wild type (wt) T4 DNA ligase. The experimental conditions were drop-down ligation cycling between 42° C. and 16° C. 96% fidelity of assembly was achieved as determined by counting 1100 colonies (per 1/10 outgrowth). This provided a high efficiency of assembly of 137,500 colonies per 25 μl of reaction.

FIG. 18B shows a comparison of BsmBl and Bsa-HFv2 yield for increasing numbers of cycles. The difference observed between the two enzymes increases with the number of cycles suggesting that BsmBl is a more efficient enzyme for assembly than Bsa-HFv2 using wtT4 DNA ligase and a cycling temperature of 42° C./16° C.

FIGS. 19A and 19B show the assembly efficiency for a T7 phage genome (40 KB) assembly from 52 fragments in a single pot assembly reaction. Wild type T4 DNA ligase and BsmB1 were combined with 52 DNA fragments contained in plasmids in a single pot. The mixture was subjected to 30 or 72 cycles at 42° C./16° C.

FIG. 19A shows the number of colonies observed after a 5-hour incubation and a 16-hour incubation.

FIG. 19B shows the plaques formed when 25 μl of assembly mix was place on a lawn of bacteria on a plate.

FIGS. 20A and 20B show T7 phage genome assembly and infectious phage reconstitution.

FIG. 20A shows a schematic of the 50 fragment T7 phage reconstitution experiment.

FIG. 20B shows results of the assembly reactions. Four replicate experiments were carried out to quantify the number of plaque forming units upon transformation of the phage gDNA assembly reactions. On average, 23 plaques were observed per pi of the assembly reaction transformed into E. coli cells.

FIGS. 21A and 21B shows that the assembled T7 page genome was active and formed plaques which were then analyzed on a gel.

FIG. 22A-22C shows a one-pot Golden Gate assembly of 52 fragments into a destination vector for lac operon assembly.

FIG. 22A shows a schematic of the 52-fragment lac operon cassette assembly. Assembly inserts were generated by PCR amplification and assembled into a destination vector containing an antibiotic resistance marker.

FIG. 22B shows an example outgrowth plate used for colorimetric scoring by reverse blue-white screening. Correctly assembled 52 insert constructs form blue colonies upon cellular transformation and incorrectly assembled constructs produce white colonies.

FIG. 22C shows results of the assembly reactions. Three replicate experiments were carried out to quantify the number of colony-forming units harboring correct and incorrect assembly products per 100 μl of E. coli outgrowth plated (0.2 μL of the assembly reaction). On average, 49% of the observed transformants harbored correctly assembled products.

FIG. 23A and FIG. 23B show that the use of the Type IIS restriction endonuclease PaqCl provided greatly enhanced efficiency in the assembly of 24 fragments

DESCRIPTION OF EMBODIMENTS

Described herein, among other things, is a computer-implemented method for selecting a set of overhangs for an assembly reaction.

Unless defined otherwise, all technical and scientific terms used herein in the molecular biology field have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Singleton, et al., DICTIONARY OF MICROBIOLOGY AND MOLECULAR BIOLOGY, 2nd ED., John Wiley and Sons, New York (1994), and Hale & Markham, THE HARPER COLLINS DICTIONARY OF BIOLOGY, Harper Perennial, N.Y. (1991) provide one of skill with the general meaning of many of the molecular biology-related terms used herein. Certain terms are used herein for which explanations are provided below.

As used herein, the term “target polynucleotide” refers to the end product of a ligation based ordered assembly of fragments that may be DNA, RNA or a mixture thereof.

As used herein, the term “polynucleotide fragments” refer to the building blocks that when assembled, create the target polynucleotide. These building blocks may be derived from sequence databases and may contain promoter sequences, enhancer sequences, coding sequences etc. Polynucleotide fragments may be made by chemical synthesis (IDT, Coralville, Iowa) or by enzymatic synthesis using for example, a terminal transferase-based synthesis. The fragments made in this way may be assembled in a preliminary step from the products of chemical and/or enzymatic synthesis to form larger polynucleotide fragments suitable for assembly into a gene. Where individual polynucleotide fragments are amplified from a template, e.g., by PCR their length does not exceed the processive capability of the polymerase used in amplification. For example, for Taq polymerase, amplicons rarely exceed 5 kb-10 kb and may have a minimum length of 15 nucleotides in length.

As used herein, the term “oligonucleotide” refers to a multimer of at least 10, e.g., at least 15 or at least 30 nucleotides. In some embodiments, an oligonucleotide may be in the range of 15-500 nucleotides in length, or more. Any oligonucleotide used herein may be composed of G, A, T and C, or bases that are capable of base pairing reliably with a complementary nucleotide.

As used herein, the term “sequence” refers to a series of letters each letter corresponding to a base e.g. A=adenine, T=thymine, U=uracil, G=guanine and C=cytosine. Modified nucleotides (nucleoside (base and deoxyribose) and a phosphate) may optionally be included in an overhang sequence and hence in a ligation efficiency database. A plurality of letters in a specific order describes figuratively the composition of a molecule.

As used herein, the terms “perfect match”, “complementary” and Watson and Crick pairs each refer to the pairing by hydrogen bonds of bases on separate strands of a duplex DNA where A is matched to a T or U and G is matched to a C.

As used herein, the term “junction” refers to a position in a target polynucleotide where component polynucleotide fragments have been joined by a ligase. The term “junction” also refers to a position in a sequence of a target polynucleotide in a database where fragmentation is recommended for assembly of a target polynucleotide from an optimized set of fragments. The context of the word “junction” will make clear which of the two meanings is intended. The assembly methods described herein may be used to create scarless junctions in the target polynucleotide meaning that the junction in the target polynucleotide would be indistinguishable from the corresponding position in the original polynucleotide sequence.

As used herein, the term “overhang” refers to a single stranded region at the end of a double stranded fragment polynucleotide for example DNA. The overhang is preferably formed by an enzyme that creates a staggered cleavage of the nucleic acid on both strands of the duplex outside the recognition region. The overhangs are generally 5′ overhangs. The overhang can be defined by its length and its sequence. For example, there are 256 different possible 4-base overhangs (4⁴). Overhangs of 2 bases, 3 bases, 4 bases and 5 bases are exemplified here, generated by restriction endonuclease cleavage. The overhang can contain 2-8 nucleotides although 3 or 4 nucleotide overhangs are generally preferable. The preference derives from the availability of restriction endonucleases (e.g., Type IIS restriction endonucleases) that cleave double stranded DNA outside the recognition site to produce 3 or 4-base overhangs and from the number of possible overhang pairs in a set which is sufficient to optimize ligation of a plurality of polynucleotide fragments to form a target polynucleotide.

Matching the overhang from one polynucleotide fragment with a second complementary overhang on a second polynucleotide fragment results in a junction if a ligase is added to the mixture. The first overhang and the second complementary overhang are referred to as overhang pairs or complementary overhangs. While not wishing to be limited by theory, it is proposed here that combining the ligase with the restriction endonuclease in a single assembly reaction mixture results in a significant reduction in inappropriate hybridization and ligation events. These inappropriate events occur when a cleavage product that consists of an overhang and the restriction endonuclease recognition sequence reconnects with the assembly fragment from which it has been cleaved or reconnects with another cleavage product. In both scenarios, the sequences are cleaved again by restriction endonucleases in the reaction mix to liberate the polynucleotide overhangs for proper ligation to the compatible polynucleotide fragment partner.

As used herein, the term “inputs” refers to the information the user enters into the computer. These may include: specified reaction conditions, a target polynucleotide sequence that can be divided into polynucleotide fragments, excluded overhangs, included overhangs, and the number of desired fragments or overhangs. Input parameters are received by the computer.

As used herein, the term “outputs” refer to instructions from the computer that enable the user to make the desired target polynucleotide. These may include: overhang sets with preferred ligation fidelity scores for a specified number of junctions, and/or full polynucleotide fragment sequences based on input of the target polynucleotide. Where polynucleotide fragment sequences are entered by user, then the computer output may include pairs of overhangs that avoid internal sites, palindromes and repeat overhangs and provide a high overall fidelity score for the specified reaction conditions including cycling conditions, incubation time and temperature and recommended enzymes for optimizing ligation fidelity. Computer outputs may further provide graphical display of fragment assembly design and fragment sequences or link to the same. A computer output may also provide a matrix of ligation frequencies for all combinations of the selected overhangs in order to graphically illustrate the predicted fidelity for a chosen set of overhangs and their complements or link to the same.

By default, the tool can provide ligation data in a graphical output, indicating the general efficiency of each connection. For example, in FIG. 11A-11B, the checkbox can be toggled to display normalized ligation counts. In multiplex ligation assay, the relative ligation frequency was experimentally determined for all 256 4-base overhangs in a single experiment. Total ligation events for each experiment were normalized to 100,000; in this case, a typical frequency for any single Watson-Crick pair was 300-400 observations per 100,000 ligation events. Further details are provided in Potapov, et al. Nucleic Acid Research, 46, e79 (2018); Potapov, et al. Cold Spring Harbor Laboratory, bioRxiv, doi: https://doi.org/10.1101/322297 (2018); and Potapov et al. ACS Synthetic Biology 711, 2665-2675 (2018).

As used herein, the term “experimental conditions” refer to choices of a ligase, endonuclease and other enzymes as desired for the workflow and their unit ratio. For example, the ligase to restriction endonuclease unit ratio may be within the range of 1:10-1:1000 regardless of the type of DNA ligase or Type IIS restriction endonuclease selected. Experimental conditions may include salt concentrations, temperature and time used to complete ligation of overhangs and may further include cycling conditions for ligation reactions. Experimental conditions may be selected to reduce the assembly time for large numbers of fragments, improve the fidelity score of the selected set of overhangs, improve the activity of the cleavage endonucleases while retaining ligase activity and performance and/or reduce background of incorrect assemblies. Experimental conditions may also affect removal of mismatches in the target polynucleotide. Watson/Crick perfect matches may be preferred although in some cases a single base mismatch in the overhang may provide a higher fidelity score for ordered assembly than a perfect match of bases that do not readily hybridize as deduced from the ligation frequency tables. Alternative splicing may also occur during assembly resulting in a mismatch at a junction. Mismatches can be removed using EndoMS or T7 Endo I, or other repair enzyme that identifies mismatches, to cleave the DNA at the mismatch.

As used herein “ligation frequency” refers to the number of times an overhang will ligate to another overhang out of a total number of ligations (e.g., 100,000 ligations).

As used herein, the term “ligation fidelity” refers to a numerical assessment of discrimination against the ligation of substrates containing mismatched base pairs bias (preferential ligation of particular sequences over others). This has been determined in various ways such as: biochemically by sequencing ligation events for a specific overhang pair (sequence analysis) to detect perfect or imperfect matches; and by counting blue colonies denoting successful ligations of target polynucleotides as a function of the total number of colonies on a plate. The ligation fidelity is then calculated from the number of correct assemblies/total number of assemblies.

As used herein, the term “ligation fidelity by overhang” or “ligation fidelity score for an individual overhang” refers to the frequency at which an individual overhang and its complement independently ligate to a perfectly complementary overhang relative to all overhangs in a set and their complements. A fidelity score can be calculated by consulting a ligation frequency table, which comprising individual experimentally-defined measurements of the number of ligation events for each overhang to all overhangs of the same length (including itself). A ligation fidelity score for an individual overhang is calculated as the number of ligation events that occur between the individual overhang and its complement relative to the total number of ligation events that occur between i. the individual overhang and all of the overhangs in the set and their complements and ii. the complement of the individual overhang and all of the overhangs in the set and their complements.

As used herein, the terms “ligation fidelity of an entire set” and “overall fidelity score” refer to the expected ratio of correctly ligated assemblies to incorrectly ligated assemblies based on the individual ligation fidelity scores for each member of a given set of overhangs. An overall fidelity score for a set of overhangs can be calculated by multiplying the individual ligation fidelity scores for the overhangs in the set together.

As used herein, the term “overall assembly fidelity” refers to the actual number of correctly assembled target nucleic acids compared to the predicted number of correctly assembled target nucleic acids. For example, the assembly efficiency of 10 oligonucleotides with overhangs can be determined by the number of times all 10 junctions are ordered correctly in the population of target polynucleotides. Assembly fidelity may be greater than 20%, 30%, 40%, 50%, 60%, 60%, 70%, 80%, or 90%.

The term “ligation efficiency” refers to the number of correct assemblies as a function of time. As used herein, the term “assembly efficiency” refers to the rate at which full length ligation products (complete target nucleic acids as determined by size or colony formation or sequencing) accumulate in a particular assembly reaction after a particular time period. An arbitrary unit of time may be selected which will provide an overall average/unit time for ordered assembly of a target polynucleotide. However, the ligation efficiency may not be linear over a selected incubation period.

The term “ligation yield” refers to the number of correct assemblies.

The term “ligation accuracy” refers to the number of correct end joining of fragments over number of total assemblies. This may be determined by sequencing.

A method described herein is for selecting a set of overhangs suitable for assembling a selected number of polynucleotide fragments into a target polynucleotide. For example, this can be achieved by means of a computer system that can test and arrange in suitable order, useful overhangs that not be achievable by a mental act. The identification of suitable overhangs may involve one or more steps. A first step may be initiated by receiving numbers that have been entered by a user into a computer interface. These numbers may include: (i) a desired number of overhangs for an assembly reaction and (ii) a length of the overhangs. In some embodiments, the number of overhangs may be in the region of 5-200, e.g., 10-100, e.g., 10-50, although the number of overhangs can be outside of these ranges in some circumstances. The length of the overhangs may be 2, 3, 4 or 5 nucleotides, where the length of the overhangs is limited only by the choice of restriction endonuclease or other means for generating the overhang and the frequency and fidelity of possible ligation reactions. The choice regarding the preferred length of overhang may be subject to the number of possible overhangs for any combination of nucleotides in the overhang where this number should exceed the number of fragments to be joined. After the desired number of overhangs for an assembly reaction and the length of the overhangs have been received, the computer provides a set of overhangs from an overhang table, of the selected length (e.g., 2, 3, 4 or 5-bases). For example, if a user were to input, into the computer, 20 overhangs each 4-bases long, then the computer would output a set of 20 unique overhangs that did not include duplicates, complements, palindromes (e.g., GATC) or excluded sequences. GATC is an example of a palindromic sequence since its reverse complement is GATC. Palindromes should be avoided because any one fragment with palindromic ends could anneal to another identical molecule resulting in the disruption of ordered assembly. The interface may permit receiving a list of one or more overhangs that should be excluded or included. Overhangs that are excluded may be selected because of poor fidelity or frequency of ligation profiles or because the overhangs have been used elsewhere in a reaction. Included overhangs may be selected on the basis of experimental findings of their high fidelity and/or frequency values. The interface may additionally permit selection or input of experimental conditions under which the assembly reaction is expected to occur. The experimental conditions will change the choice of ligation frequency tables and individual overhang ligation fidelity determinations accessed by the computer.

As would be apparent, the overhang ligation frequency table may be stored in computer memory and can include all possible overhangs of the desired length or a subset of the same. For example, for a 4-base overhang the overhang table may contain 256 4-base sequences for a 3-base overhang the overhang table may contain 64 3-base sequences. The overhangs may be selected in any particular order. For example, in some embodiments the overhangs may be selected randomly whereas in other embodiments the overhangs may be selected in a defined order.

Next, after a set of overhangs of the desired length and number have been selected, then the computer calculates a ligation fidelity score for each individual overhang and its complement in the set. For example, if there are 20 overhangs in the set, then there should be 20 ligation fidelity scores, where the ligation fidelity score of each individual overhang represents the frequency at which the individual overhang and its complement independently ligate to a perfectly complementary overhang relative to all overhangs in the set and their complements. For example, if a particular overhang and its complement ligate together 90% of the time relative to all overhangs in the set and their complements, then that overhang may have a calculated ligation fidelity score of 0.9. This step may be done by consulting a ligation frequency table comprising individual experimentally-defined measurements of the number of ligation events. A ligation frequency table for a 4-base overhang should have an experimental value for each of all possible combinations of overhangs, i.e., 256×256/2 datapoints, each value indicating the frequency of ligation of two overhangs under defined experimental conditions. Details for how this data can be obtained is described below as well as in, e.g., Potapov et al (2018). The ligation fidelity score for an individual overhang can be calculated as the number of ligation events that occur between the individual overhang and its complement relative to the total number of ligation events that occur between i. the individual overhang and all of the overhangs in the set and their complements and ii. the complement of the individual overhang and all of the overhangs in the set and their complements.

The overall fidelity score for the set of overhangs can then be generated based on the calculated ligation fidelity score for each of the individual overhangs, as output above. In some embodiments, the individual ligation fidelity score may be multiplied together to obtain the overall fidelity score. For example, if there are 20 overhangs that each have a fidelity of 0.950, then the overall fidelity score for that set of overhangs may be 0.36 (i.e., 0.95²⁰). In some embodiments, this calculation may, in addition, weight overhangs by how efficient an overhang is at ligating to its complement. For example, in some cases, two overhangs may have equal fidelities, but one ligates to its complement more efficiently than the other under the conditions used. In this case, the overhang that ligates with a higher efficiency may have a higher weight than the other. As such, in some embodiments, the overall fidelity score may be calculated using i. the calculated ligation fidelity score for each of the individual overhangs and ii. the yield that each of the individual overhangs ligates to a perfectly complementary overhang.

After an overall fidelity score for the selected set of overhangs has been calculated, the process may be repeated for another set of overhangs to calculate a plurality of overall fidelity scores, each for a different set of overhangs. In this step the sets of overhangs selected in the iterated steps are different from one another (and different from the first set of overhangs). Again, in the iterated steps the selection may be random or in a defined order. In some embodiments, these steps may be iterated using a Monte Carlo simulation. In this method, at least 100, at least 1,000 or at least 10,000 overall fidelity scores may be generated, each for a different set of overhangs. This part of the method repeated until an overall fidelity score has been assigned to all possible combinations of overhangs or until one or more overhangs have been identified that overall fidelity score that is above a threshold.

After the overall fidelity scores have been calculated, then the method may comprise identifying the set of overhangs that has a suitable overall fidelity score. In some embodiments, the identified set of overhangs may have an overall fidelity score that is in the top 50%, top 20%, top 10% or top 5% of overall fidelity scores. In some embodiments, the identified set of overhangs may have the highest overall fidelity score or a score that is in the top 10 or top 5 highest fidelity scores. The selected set of overhangs may be output from the computer onto, e.g., a display.

Where ligation conditions (in addition to the desired number of overhangs for an assembly reaction and the length of the overhangs) are received in the interface, the overall fidelity scores are calculated for the overhangs in ligations that were performed in the specified ligation conditions. Hence a ligation frequency table that corresponds to the specified conditions may be selected from multiple ligation frequency tables, each for a different ligation condition. After the ligation frequency table is selected, then the ligation fidelity scores can be calculated using data in that table. Accordingly, the ligation conditions may comprise one or more of a ligase, a salt concentration, a temperature, temperature range and/or thermocycling conditions (which may be used for cleavage and ligation). These options could be implemented using a drop-down menu, where the options laid out in the drop-down menu correspond to different ligation frequency tables. Examples of experimental conditions that were found to affect ligation efficiency, fidelity and yield are provided in Table 8 and are discussed in more detail below. The parameters experimentally tested for yield, fidelity and efficiency of ordered assembly included the following in various combinations:

-   -   (a) Temperature conditions for ligation including static         temperatures and cycling between high and low temperatures using         drop-down or touch-down cycling. These terms are explained in         Example 2;     -   (b) Number of fragments for ordered assembly;     -   (c) Length of overhang;     -   (d) Time of incubation of the restriction endonuclease/ligation         reaction;     -   (e) Types of restriction endonuclease and ligase;     -   (f) Salt concentrations of the buffer;     -   (g) Additional proteins for repairing mismatches.

In variations of the method, a first step may include receiving a nucleotide sequence of an intended assembly and a set of intervals (e.g., at least 5, at least 10, at least 20 or at least 30, up to 50 or more intervals) in which the nucleotide sequence can be cleaved (in addition to the desired number of overhangs for an assembly reaction and the length of the overhangs). The input sequence may be, for example, any sequence that is at least 500 bases in length, although sequences as short as 25 nucleotides could be selected providing a Type IIS restriction endonuclease recognition (binding) sequence is present at the beginning and end of that interval. For example, the method may include receiving a sequence and multiple sets of beginning and end coordinates, where each set of beginning and end coordinates defines an interval in which the sequence can be cleaved. In these circumstances, only overhangs that are in the intervals may be selected from the overhang table such that, together, each interval is represented by a selected overhang. A non-redundant set of sub-sequences are then identified in the intervals that are the same length as the received overhang length. These sub-sequences may be stored as the overhang table itself or only sequences from the non-redundant set of sub-sequences will be selected from an overhang table. The intervals may be input into the computer by a user, e.g., by inputting the intervals into an interface, as illustrated in FIG. 17. Alternatively, a user may input a sequence and specify how many fragments are desired. In these embodiments, an algorithm may determine approximate positions at which the input sequence may be split to produce the desired number of fragments, and then identify intervals (which may be, e.g., 10-50 or 10-100 nucleotides in length) that contain the approximate positions. The intervals may be processed as described above. In these embodiments, the method may further comprise splitting the nucleotide sequence of the assembly at the identified overhangs, thereby producing a set of fragments of the assembly, where the ends of the fragments are defined by the identified overhangs.

In any of the examples provided herein, the method may comprise a user inputting into an interface, one or more of the following: (i) the desired number of overhangs for an assembly reaction, (ii) the length of the overhangs; optionally, (iii) the nucleotide sequence of the assembly (iv) the set of intervals in which the nucleotide sequence of (iii) can be cleaved, causing the method to be executed and then receiving as output, an identified set of overhangs and/or receiving a set of fragments for the assembly, where the ends of the fragments are defined by the identified set of overhangs, depending on which information is input into the interface. This method may further include receiving instructions regarding the ligation conditions for ligating the set of overhangs or fragments containing the same, and, optionally, thermocycling conditions for producing the fragments and ligating them together. In these embodiments, the method may comprise making a set of double stranded nucleic acids that have a set of overhangs that has an overall ligation score that is at or above a threshold, and their complements, and then ligating the fragments together in a single reaction to produce an assembly, wherein in the reaction the overhangs determine the order of the fragments in the assembly. The ligating may be done by overhang-directed ligation, which will be explained in greater detail above and/or below. As would be apparent the method may further comprise receiving selected experimental conditions for ligation.

FIG. 14 illustrates a user interface that can be used to input the parameters that are received by the present method. In this example, a user can specify any one or more of the overhang lengths, the size of the set (i.e., the number of overhangs that should be in the set), ligation conditions and, optionally, overhangs that should be required or excluded in the set.

FIG. 15 illustrates an example of the output of the present method. In this example, the method may output the set of overhangs, the calculated overall ligation fidelity for the set, and a fidelity matrix that shows the efficiency of ligation for each overhang in the set and their complements to all overhangs in the set and their complements.

FIG. 16 illustrates another user interface that can be used to input the parameters that are received by the present method. In this example, a user can input a sequence, ligations conditions and define regions where the sequence can be split and, optionally, overhangs that should be required or excluded in the set.

FIG. 17 illustrates an example of the output of this example. In this example, the method may output the set of overhangs, the calculated overall ligation fidelity for the set, and a fidelity matrix that shows the efficiency of ligation for each overhang in the set and their complements to all overhangs in the set and their complements, as well as the sequences of the fragments that have the selected overhangs at the ends.

Embodiments are provided herein for enabling a user of a computer to review by means of a graphical representation, the ligation fidelity profile expected from a predetermined set of fragment overhangs under selected experimental conditions. Each of these features can be modified by adjusting any of the parameters described herein to provide a revised graphical representation and to determine whether the change improved the ligation fidelity profile for the selected number of overhang sequences using the graphical representation of the deviation from perfect score obtained for the set of overhang sequences.

Other embodiments are provided herein for enabling a user of a computer to rapidly and efficiently obtain from the computer an optimized set of overhang sequences suited for assembling multiple nucleic acid fragments into a target polynucleotide. The optimization relies on a database of ligation fidelity values for all possible overhang sequences for a complete set of all possible sequence combinations of overhangs having a single length. The complete set of overhangs may include overhangs of different sizes. The nucleic acids include DNA, RNA or DNA/RNA hybrids or chimera. While DNA may be specifically mentioned in the description, examples and claims for convenience, embodiments herein are not limited to DNA but may be applied to any type of nucleic acid as described above.

The overhang length of choice may be determined by the availability of endonucleases that generate the desired overhang length. Another factor is the frequency of recognition sequences in the originator DNA and the adjacent sequences. For example, recognition sequences that occur within a polynucleotide fragment should be avoided. The length of the recognition sequence determines to some extent at least, the likelihood of it appearing at internal sites within the originator DNA. For example, a 7-base recognition sequence is predicted to occur less frequently than a 6-base recognition sequence. An 8-base recognition sequence is predicted to occur even less frequently than a seven base recognition sequence. Consequently, the use of 6-base, 7-base and 8-base recognition sequences for Type IIS restriction endonucleases that generate overhangs after cleavage of 3, 4 or 5-base overhangs are preferred. Examples of 7-base recognition sequences for IIS restriction endonucleases include Aartl and its isoschizomers including PaqCl. These endonucleases cleave DNA outside their recognition sequence to produce a 4-base overhang.

An increasing number of different Type IIS restriction endonucleases are being described. Many of the current endonucleases may be found in the commercial literature (including www.neb.com) provided by New England Biolabs (NEB), including recognition sequences and length of overhang generated by cleavage. New endonucleases are listed in a regularly updated database (see REBASE on www.neb.com from New England Biolabs). For example, this includes Acul, Alwl, Bael, Bbsl, Bbnl, Bccl, Bcgl, BciVl, BcoDl, BspMl, BfuAl, Bmrl, Bpml, BpuEl, Bsal, BsaXl, BseRl, Bsgl, BsmAl, BsmBl, BsmFl, BspCNl, BspMl, BspQl, BsrDl, Bsrl, BtgZl, BtsCl, BtslMutl, CspCl, Earl, Ecil, Esp3l, Faul, Fokl, Hgal, HpHl, HpyAv, Mboll, Mlyl, Mmel, Mnll, NmeAlll, Plel, Sapl, and SfaNl. These endonucleases are all available from New England Biolabs. The recognition sequences and overhangs are described by NEB along with reaction buffers, reaction temperatures and storage conditions. Isoschizomer information is also provided.

PaqCl, described herein as having at least 90% sequence identity to SEQ ID NO:26 is a novel Type IIS restriction endonuclease and as FIG. 23A-23B shows, it is a preferred Type IIS restriction endonucleases for performing assembly of large numbers of fragments (at least 20 fragments). Unlike Aarl, it does not appear to have star activity that is detectable by gel electrophoresis and cuts DNA to completion. PaqCl appears to perform better in the presence of a synthetic oligonucleotide. Also described herein is an activator oligonucleotide that was found to improve the activity of PaqCl. This oligonucleotide is a synthetic self-complementary oligonucleotide that comprises a double-stranded region and a loop, wherein the double-stranded region contains a binding (recognition) sequence for PaqCl and wherein the oligonucleotide comprises unligatable 3′ and 5′ ends and cannot be cleaved by PaqCl.

Recognition sequences can be readily introduced at the termini of fragments by primer dependent amplification or by chemical nucleic acid synthesis. The sequences adjacent to the restriction endonuclease recognition sequence form the overhangs. Preferably, these should be suitable for joining an ordered set of fragments that comprise a target nucleic acid.

Factors for determining an appropriate length of overhangs include: how many fragments are desired to be joined where the longer the overhang, the larger the set of possible combinations. This enables more fragments, each with a unique overhang complementary to its adjacent fragment overhang, to be joined to form a target polynucleotide. Other factors include the efficiency of melting/annealing where shorter overhangs melt and anneal faster and longer overhangs require higher melting temperatures. Ligation efficiency is another factor where longer overhangs may ligate more efficiently than shorter overhangs. Ligation efficiency also depends on the characteristics of the nucleotides singly or together in the overhang where some sequences are more efficiently hybridized and/or ligated to form a junction than others, have reduced bias and do not favor or induce mismatches.

In one embodiment, the output from the system instructs the user which restriction endonucleases should be used to cleave the nucleic acid to generate overhangs having sequences that have been optimized for ligation fidelity or selected for a chosen ligation fidelity. However other cleavage enzyme systems can be used such as uracil-specific excision reagent (USER®, New England Biolabs, Ipswich, Mass.), argonautes, clustered regularly interspaced short palindromic repeats (CRISPR) or other cleavage enzymes can be used to generate overhangs.

The experimental conditions may be offered by menu from the computer interface to the user and then selected by the user or selected by the computer that has computed all the various parameters for the assembly and provides the best conditions for efficient joining all the fragments in a set correctly. The use of a Type IIS restriction enzyme enables the precise selection of a site where the DNA will be broken and enables exclusion of the restriction enzyme recognition sequence from the final construct (thus enabling seamless one-tube assembly reactions) or certain types of nucleic acid assembly, for example for gene coding regions, scarless junctions which do not alter the DNA sequence are important. In other applications, for example, cistron formation, additional or altered nucleotides that may remain from an assembly reaction may not interfere with the gene expression of the target nucleic acid. In one embodiment; the endonucleases suitable for use in generating overhangs and scarless junctions include: 2-base overhang generators (e.g. Btsl and isoschizomers thereof, Acul and isoschizomers thereof), 3-base overhang generators (e.g., Sapl and isoschizomers thereof (7-base recognition) and BspQl and isoschizomers thereof (7-base recognition)), 4-base overhang generators (e.g., Bsal-HFv2 and isoschizomers thereof (6-base recognition), Bbsl and isoschizomers thereof (6-base recognition), BsmBl and isoschizomers thereof (6-base recognition), Aarl and isoschizomers thereof) and 5-base overhang generators (e.g., Hgal and isoschizomers thereof with a 5-base recognition site). Other restriction endonucleases as described in the New England Biolabs 2017/2018 catalog and isoschizomers thereof may be used for those assembly reactions that are not required to be scarless.

In some embodiments, overhangs are created using alternate enzymes such as nicking agents for example, USER (also see for example U.S. Pat. No. 7,435,572), or EndoMS suitable for creating overhangs in DNA fragments; and argonautes and Cas cleavage enzymes suitable for overhangs in DNA and RNA, where these enzymes utilize guide DNAs or RNAs.

Embodiments describe how to obtain an optimized data set by profiling end-joining hybridization and ligation fidelity and bias to predict highly accurate sets of connections for ligation-based DNA assembly methods. Unlike the prior teachings that preferred at least a two base pair difference between overhangs, to avoid overhangs with 3 identical base pairs in a row, and to ensure all overhangs have similar GC content in a given assembly (Nilsson et al. Nucleic Acids Res., 10, 1425-1437 (1982); Goffin et al. Nucleic Acids Res., 15, 8755-8771 (1987); and Wu et al. Gene, 76, 245-254 (1989)), the optimized data sets exemplified herein have no such rule based limitations. This presents a significant improvement over the prior art rules that restrict the user to a limited number of 4-base overhangs, which is particularly constraining when sequences may not be chosen arbitrarily (e.g., when assemblies must break within coding sequences).

The optimized data set avoids the use of any overhangs more than once within an assembly, and palindromic overhangs to prevent self-ligation of fragments and depends on quantification of sequence-dependent ligation fidelity and identification of mismatch-prone pairings to limit mismatches. In one embodiment, ligation fidelity profiles were generated that accurately predicted junction fidelity in 10-fragment Golden Gate assembly reactions. The ligation fidelity profiles were verified by determining the efficiency of assembly of a lac cassette from up to 24-fragments in a single reaction. Application of the ligation fidelity profile permitted an informed choice of junctions and enabled a highly flexible assembly design using more than 20 fragments in a single reaction.

Two-base overhangs generate a 16×16 matrix data table, 3-base overhangs generate 64×64 matrix data table, 4-base overhangs generate 256×256 matrix data table, 5-base overhangs generate a 1024×1024 matrix data table, 6-base overhangs generate a 4096×4096 matrix data table. The upper limit of overhang length using a Type IIS restriction endonuclease may be 5, 6, 7 or 8-bases in length. For a nicking agent such as USER, the number of bases in an overhang may be as much as the user desires based on the positioning of a uracil. The optimized sets of Watson crick pair overhangs include overhang pairs that can ligate with their exact complementary partner efficiently, are not palindromes, and are unique within the set. Other overhang pairs are acceptable as long as preferably no individual overhang forms a ligation product with an overhang partner containing one or more mismatches but preferably no more than one mismatch. The highest fidelity set of overhangs with good ligation fidelity can be provided by the computer for any chosen number of junctions (such as 10 junctions, 12 junctions, 15 junctions, 20 junctions etc.). The greater the number of junctions the lower the mean maximal ligation fidelity for the set of overhang pairs.

In one embodiment, the database contains the results of experimentally determined ligation and stores ligation fidelity and/or ligation efficiency parameters for all combinations of an overhang sequence of a single defined length or all combinations for each overhang length of multiple defined lengths. In all cases, the ligation parameters are specified for each pair of same length overhangs in a matrix of all possible options. These ligation parameters may include ligation efficiencies in specified buffer and temperature and time incubation conditions (for hybridization/ligation) as well as number of temperature cycles to complete ligation for a particular ligase.

Embodiments of the methods permits the user to receive a computational output that provides optimized sets of overhangs based on a measure of the net effect of cutting, melting, annealing, and ligation for a particular combination of cleaving enzyme and one or more ligases under a given set of cycling conditions where some or all of these features are provided by the user. The output can then provide a relative ligation efficiency and/or ligation fidelity value for every overhang pairing.

The computational output may additionally provide for the user an optimized protocol for performing an assembly to obtain a desired overall ligation fidelity detailing at least one of temperature, time for hybridization, cycling conditions for ligation, and buffer.

The computational output may include a graphical output of features that include one or more of the following: (1) the entire assembled sequence with the junction sites highlighted, (2) a map of input fragments with individual cut sites indicated on the fragment where the set of cut sites have been determined computationally to yield the optimal set of overhangs for fragment assembly to form the desired product; (3) a matrix of ligation fidelity of the selected overhangs under the user specified conditions or the computer optimized experimental conditions; and (4) a set of primer sequencers that contain selected Type IIS restriction endonuclease recognition sequences and overhang sequences plus any additional target fragment sequences for directing automated oligonucleotide synthesis. The set of primer sequences can be forwarded electronically to a receiving location for instructing a DNA synthesis instrument to make such primers.

In one embodiment, the results for a user's chosen set of overhangs can be optimized by the user providing the preferred set of conditions to achieve efficient and accurate hybridization. Short linkers of arbitrary sequences are preferred for large numbers of fragments (e.g., >20). Multiple data sets can be accessed that provide overhang optima under different conditions. Such assays enable the user to select a set of enzymes and reaction conditions that would give the highest possible fidelity and efficiency for a selected set of overhangs.

In another embodiment, partial overhang pair reaction parameters and data sets could be selected by the user and partial overhang reaction parameters and optionally data sets could be selected by the computer to provide the optimal ligation efficiency and fidelity possible to create the desired number of ligated fragments. For example, 15 junction pairs might be required in total to join 16 fragments of double stranded nucleic acid fragments where 6 overhang pairs had been selected by the user and the remainder of overhangs are provided in a computer-generated output optionally with preferred experimental conditions including choice of ligase. The user could then be enabled to receive an additional optimized 9 overhang pairs with optional choice of reaction components such as restriction enzyme, ligase and optional choice of other reaction conditions including cycling time and temperature that would provide the highest ligation fidelity and efficiency possible for the 15-member final set.

In another embodiment, the user inputs into the computer, a gene, gene pathway, plasmid or chromosome sequence for dividing into fragments suitable for efficient assemble with high fidelity using an optimized set of overhangs. The user may specify the target nucleic acid and the desired number of fragments. The webtool or graphical interface provides the sequence for the desired number of fragments at the optimal junctions that satisfy the hybridization parameters of the associated overhangs that when ligated, form scarless junctions thus enabling to the user to make the target polynucleotide in the desired manner. If the user additional specifies the minimum acceptable fidelity, the sequence specification for the desired number of fragments may be altered and indeed the number of fragments provided to the user might change to provide the maximum number of sequences possible with junctions that provide the specified minimum acceptable fidelity.

In another embodiment, the user may provide the target sequence and additionally may specify some junctions to be included in the design of constituent fragments with predetermined overhangs, and some subset of reaction conditions (or all reaction conditions). The computer provides to the user, a list of overhangs for efficient ligation to supply the best additional junctions and/or reaction conditions.

The assembly proceeds at either a single temperature suitable for all types of enzyme activities used in a reaction (e.g., cleavage enzymes and ligation enzymes) or any number of cycling conditions varying between an optimal cutting/melting temperature and an optimal annealing/ligation temperature. Thus, overhangs are generated and sealed in one pot, and multiple fragments can be joined together in one experiment.

As used herein, the term “ligase” refers to an enzyme that is capable of joining two polynucleotides covalently. Many different ligases have been described in the art and are widely known (see Ellenberger et al. Annual Review in Biochemistry, 77, 313-338 (2008); Bauer et al. PLOS ONE, 10, 12:e0145046 (2017)). Ligases for use in assembly reactions may include ATP ligases and NAD+ligases such as T4 DNA ligase, T7 DNA ligase, Taq DNA ligase, viral ligases such as chlorella virus DNA ligase (e.g., PBVC-1 ligase), bacterial ligases such as bacterial LigA (e.g., E. coli DNA ligase) and LigD; archeal ligases such as Thermos thermophilus (Tth) Ligase and eukaryotic ligases such as Mammalian Lig1 and Lig3. T4 DNA ligase and mutants thereof has been used in the present examples, but the methods described herein are applicable to any ligase known in the art suitable for repairing a break in the DNA backbone by joining a 5′ phosphate on one strand to a 3′ OH on a second strand in cis.

As used herein, the term “restriction endonuclease” refers to an enzyme that is used for bacterial host defense by recognizing a specific sequence on an incoming viral DNA and cleaving the DNA either at the recognition sequence or at a distinct sequence site. One group of restriction endonucleases are identified as Type IIS. This group recognizes asymmetric DNA sequences and cleaves the DNA at a site outside the cleavage site that is at a defined distance from the recognition site usually between 1 and 20 nucleotides. Restriction endonucleases share little amino acid homology. However, those endonucleases that recognize the same DNA sequences are referred to as isoschizomers. Isochizomers may cleave DNA at the same or different positions. A subset of isoschizomers are neoschizomers, recognize the same site as another endoncuclease but cleave at a different site. The term “restriction endonucleases and isoschizomers thereof” is intended to encompass those restriction endonucleases which have the same recognition sequences. For example, PaqC1 is a novel Type IIS restriction endonuclease with a sequence that is at least 90% identical to SEQ ID NO:26 below. Every restriction endonuclease is encoded by a DNA sequence that has little homology with an isoschizomer to itself. The differences in sequences have been long acknowledged and is firmly established in REBASE, the definitive restriction endonuclease database provided by New England Biolabs. Any restriction endonuclease with 90% or greater sequence homology refers only to minor mutations introduced into the selected restriction endonuclease sequence. Aarl is a functionally similar Type IIS restriction endonuclease with a 7-base recognition sequence (CACCTGC) that cleaves double strand DNA to create a 4-base overhang. The full DNA sequence encoding Aarl is unknown but fragments of sequence indicate that there is little sequence identity with PaqCl

Unlike Aarl, PaqCl does not have detectable star activity and appears to be a more active cleavage enzyme. This naturally occurring restriction endonuclease appears to be enhanced by the use of a synthetic oligonucleotide that acts as an activator for this restriction endonuclease. The self-complementary oligonucleotide that comprises a double-stranded region and a loop is preferably less than 100 nucleotides in length and contains the recognition sequence for PaqCl and extends no more than 0-4 bases downstream from the recognition sequence plus one unnatural extension of a blocking moiety on each strand. The synthetic oligonucleotide also preferably contains a ligation inhibiting modified base at the 5′ end such as an inverted dideoxy thymine (invddT) and a ligation block at the 3′ end such as a 3′ dideoxy-C, 3′ C3 Spacer (C3-OH), a C6 spacer or 3′ Amino Linker (C6-NH2). While not wishing to be limited by theory, it is proposed that the PaqCl binds this synthetic oligonucleotide and diffuses through 3D space to complex with the PaqCl this is bound to the substrate DNA resulting in cutting competent complexes that allow cutting of the substrate target.

PaqCI sequence  (SEQ ID NO: 26) 510 aa MPYDHNAEADFAASEVARMLVADPGLCYDAASLPASISASASYEPSAAGW PKADGLVSVLEGGTSTQRAIALEYKRPQEGIHGLLTAIGQAHGYLHKGYS GAAIVIPGRYSSHPTPAEYVRDVLNAISGSRAIAVFSYSPPDTTSPTPFA GRIQCVRPLVFDAGRVHLRPANQGPKTQWVHMREGSTTRDAFFRFLQVAK RLSADPTAPRPTLRSELVAAIGRLAPGRDPIEYITNTADNKFLTKVWQFF WLEWLATPAVLTPWKLEAGVYSAPGARTRILREDGTDFSQLWEGRVNSLK ETIAGMLNRGEISEAQGWEAFVGGISATGGGQDKQGVRARAHSYREDIDS ALAQLRWIEDDGLPTDQGYRFMTICERYGGANSRAAIDYMGATLIQTGRY ASFLHYINRLSERKFAENPLAYTKPGPGGMPVFTEESYWEYLQDLETKLT DELRVMRKVSGRARPRVRTTFQVELTLLRNYGFVSSTRHRLGVGIPIDWE QVVQALNVDL

Present embodiments describe how to determine which mismatches to expect in end-joining and to use this information to identify appropriate overhangs for ordered assembly of polynucleotide fragments using T4 DNA ligase. Ligation frequency using T4 DNA ligases have been comprehensively determined by sequencing for 2-base overhangs, 3-base overhangs, 4-base overhangs and 5-base overhangs under a standard set of experimental conditions (see Tables 3-6).

These ligation frequency tables (Tables 3-6) revealed ligation biases for T4 DNA ligases for different length overhangs under specified conditions. Sequence type and context was found to affect fidelity of ligation of overhangs at a junction, in addition to the annealing strength and/or number of hydrogen bonds of the overhang to its complement.

In general, ligases are tolerant of mismatches at the side of the junction providing the 5′-phosphate. T4 DNA ligase could ligate all mismatched base pairings at the 5′ side, but preferred C:T, G:T, A:C and T:T mismatches at the 3′-hydroxyl side to the exclusion of others. The high-fidelity Tth DNA ligase was less tolerant of mismatches on the 5′-side of the ligation junction than T4 DNA ligase, readily ligating T:T, T:G, A:C and C:A mismatches, with lesser amounts of G:T, C:C, A:A and G:A ligation. Asymmetrical preferences were found to be common in ligation mismatch tolerance; for example, T4 DNA ligase prefers T:C to C:T at the 3′-OH side of the junction, and Tth DNA ligase prefers T:G to G:T at the 5′-side of the ligation junction. In one embodiment, the relative frequency of all ligation products after T4 DNA ligation were identified with or without mismatches, the position-dependent frequency of each mismatch, and the surprising observation that 5′-TNA overhangs ligate extremely inefficiently compared to all other Watson-Crick pairings.

GC rich overhangs were found to display a higher frequency of mismatch ligation, especially when two of 3-bases in the overhang formed G:C Watson-Crick pairs. Among overhangs with single base mismatches, the two correct base pairings were both G:Cs in 50% of cases, G:Cs and A:Ts in 42% of cases, and both A:Ts in 8% of cases at 25° C. (with similar ratios at 37° C.). Not only the GC content but also the location of G:Cs had an effect on the likelihood of mismatch ligation. For example, overhangs with single-base edge mismatches containing middle A:T pairs and edge G:C base pairs (XAG/YTC, where X:Y indicates mismatch) outnumbered the reverse (XGA/YCT) by a factor of 2.5 (32% versus 13%, respectively), despite having similar predicted AG of annealing (Potapov et al. Nucleic Acid Research, 46, e79 (2018); and Potapov et al. Cold Spring Harbor Laboratory, bioRxiv, doi: https://doi.org/10.1101/322297 (2018)).

The results provided herein from sequencing studies (see for example, Example 1) show that mismatches for 3-base overhangs were observed for A:G, A:C, A:A, T:T, and G:T. G:T mismatches were much more (˜10-fold) prone to ligation than T:G, and A:C mismatches which in turn were much more prone to ligation than C:A (˜40-fold). Mismatches in the middle position were very poorly tolerated (2.3% of all ligation events), with overall incidence much lower than at the edge positions and only T:T mismatches present in relative high frequency (36% of all mismatches at this position; FIG. 6C).

In addition to the effect of base composition of the overhangs on ligation frequency and fidelity, the base composition of the overhang may also have an effect on efficiency of ligation which is measured by yield over time. It was noted that the ligation rate of TNA overhangs was relatively very slow compared to all other Watson-Crick pairings, including ANT and other high AT overhangs. Incubation time required for ligation may become increasingly important when more fragments above 25 fragments are to be assembled into a target polynucleotide. Selection of overhangs by sequence as determined by a computer after receiving various inputs at an interface are shown here to be effective in rapidly profiling the ligation fidelity of T4 DNA ligase for a plurality of overhangs in a single experiment.

Other factors in addition to the sequence and type of overhang that can increase fidelity (reducing mismatches and/or bias) at ligation junctions during assembly of polynucleotide fragments include one or more of the following: combining ligase with restriction endonuclease in a single reaction; increasing ligation temperature; increasing salt concentration such as ionic strength, divalent cation concentration buffer pH; temperature cycling and varying the conditions thereof; and adding a repair enzyme to correct mismatches that may occur.

5′deadenylase may be used to enhance ligation. One example of a deadenylase is aprataxin. Although the use of the term “aprataxin” is generally the name given to the human derived deadenylase, it is here used interchangeably with “deadenylase” from the family of the histidine triad (HIT) superfamily. This is a conserved family where for example yeast deadenylase is referred to below as aprataxin-like.

Deadenylase-Aprataxin, Genbank ID: Q7Z2E3, from Homo sapiens (SEQ ID NO: 18) MSNVNLSVSDFWRVMMRVCWLVRQDSRHQRIRLPHLEAVVIGRGPETKIT DKKCSRQQVQLKAECNKGYVKVKQVGVNPTSIDSVVIGKDQEVKLQPGQV LHMVNELYPYIVEFEEEAKNPGLETHRKRKRSGNSDSIERDAAQEAEAGT GLEPGSNSGQCSVPLKKGKDAPIKKESLGHWSQGLKISMQDPKMQVYKDE QVVVIKDKYPKARYHWLVLPWTSISSLKAVAREHLELLKHMHTVGEKVIV DFAGSSKLRFRLGYHAIPSMSHVHLHVISQDFDSPCLKNKKHWNSFNTEY FLESQAVIEMVQEAGRVTVRDGMPELLKLPLRCHECQQLLPSIPQLKEHL RKHWTQ Deadenylase: Genbank ID: Q08702, from Saccharomyces cerevisiae (SEQ ID NO: 19) MSWRYALKNYVTSPETVNDDTVTYFDDKVSIIRDSFPKSECHLLILPRTM QLSRSHPTKVIDAKFKNEFESYVNSAIDHIFRHFQEKFRIKKSDDDKDPC WDDILKDKNKFVRNFVQVGIHSVPSMANLHIHVISKDFHSVRLKNKKHYN SFNTGFFISWDDLPLNGKNLGTDKEIETTYLKEHDLLCCYCQRNFSNKFS LLKKHLELEFNSHFELK Deadenylase: Genbank ID: O74859, from Schizosaccharomyces pombe (SEQ ID NO: 20) MSVHKTNDAFKVLMNSAKEPIVEDIPKKYRKQSFRDNLKVYIESPESYKN VIYYDDDVVLVRDMFPKSKMHLLLMTRDPHLTHVHPLEIMMKHRSLVEKL VSYVQGDLSGLIFDEARNCLSQQLTNEALCNYIKVGFHAGPSMNNLHLHI MTLDHVSPSLKNSAHYISFTSPFFVKIDTPTSNLPTRGTLTSLFQEDLKC WRCGETFGRHFTKLKAHLQEEYDDWLDKSVSM Deadenylase: Genbank ID: XP_003666069, from Thermothelomyces thermophilus (SEQ ID NO: 21) MAERAEDADDIPQPESAPPTTDQQQQQQHDSPPPKAPAKRNAFEELMAPK PKAPISQAPQFLAHKASQVIRGVWRGALIEYIEHPERFPDKVLRVTADTV LIKDAFPKATVHLLLLPRSPAHYLVHPHDAFADPAFLAMMRGEAAVAAEL AAAELARRLGSFSASNRARDEAMSRGVGPDQLPPGRDYSRDIRVGTHAHP SMAHLHVHVISRDMRSEKLKHRKHYNSFNTPFFVPLEDHPLAQDDVRRQT GYQNGNLAKDLVCWRCGKGFGNRFAELKRHLEDEFEKWRAE Deadenylase: Genbank ID: XP_003652653, from Thermothielavioides terrestris (SEQ ID NO: 22) MAETAEDLEDLTRTESVASSADSPESTPKQDEAQTPTARANTTKPSKPET KRNAFTELMAPKPRAPISQAPQSLASKASQVIRGVWRGALIEYIEHPERF PNQVLRVTAHTVLIKDAFPKSTIHLLLLPRSPAHYLLHPHTAFADASFLT TIRAEAAEAARLAAAELARQLGSFSASNRARDEAVGRGVPPDRLPPGRDY AREIRVGTHAHPSMAHLHVHIISRDMRSERVKHRKHYNSFNTPFFVPLAD YPLAEDDVRRETGYQNANLRRELVCWRCGRTFGNRFAELKRHLEEEFVEW RAE Deadenylase: Genbank ID: SPQ25427, from Thermothielavioides terrestris (SEQ ID NO: 23) MRVYVHVGGPLHAGLDEVPVCVDLITEAFLGAPVNTLEASEEVEGVTKEG TRTYRLIDIQHILASKLAAFCARGDLDSHDFLDLMWLLIKSPYSVKLREG SVNVPLDQRQAFLAAASTESPHIPSPQSLASKASQVIRGVWRGALIEYIE HPERFPNQVLRVTAHTVLIKDAFPKSTIHLLLLPRSPAHYLLHPHTAFAD ASFLTTIRAEAAEAARLAAAELARQLGSFSASNRARDEAVGRGVPPDRLP PGRDYAREIRVGTHAHPSMAHLHVHIISRDMRSERVKHRKHYNSFNTPFF VPLADYPLAEDDVRRETGYQNANLRRELVCWRCGRAFGNRFAELKRHLEE EFVEWRAE Deadenylase: Genbank ID: XP_006694125 from Chaetomium thermophilum var. thermophilum DSM 1495 ((SEQ ID NO: 24) MPEAEIPEEMDEFVQPESAPPTVDSPEVPVDHDATKTVSSVLETFTSTKK DAFAELMSHKQPSKKLMKPPRSLAEKAGKVIGGVWRGALGPFIEHPEKYP DQVLRVTEHTVLIKDRYPKATIHLLLLPRSKEHNLLHPHTAMADPAFLKI MRAEAETAAQLAAAELQRLLGRFSEKNRSRNEAIDACVPFDELPPGRDYR KDIRVGTHAHPSMAHVHVHIISRDMRSESLKRVKHYNSFNTPFFIPLEDY PLGEEDERWSTSYQNNNLTGDMVCWRCKKNFGHKFAELKRHLEEEFEAWK RE Deadenylase:, Genbank ID: XP_003662779, from Thermothelomyces thermophilus ATCC 42464 (SEQ ID NO: 25) MVRPYDPTLTETAVRVDPRDSREYAGNQEASPLYDICHHPEKYTNVRYFD REMVVLDDANAKSPDHVILMPRDTSIKEMACLKTKHLPLLYRFRDQAHRE IERMMRVDPGRIPMFRVGFHTIPSLFPLHCHVHDCSLSTDKMFHARHWKV NFSNMFVALDRVIEEIERTGRIEVDADAYRHDWRTRPIRCPVCPGRQPQW EADITELAAHWRRHVDEWKSGRAPLPPNVTPARLWEPSYPVILTTRRRSG FLGLLGDELDHLKAEFPGLEIHSYYTDEWPRIPKYVLDKTTVYLSAAELP PPGYSLPRLEWVHLGSSGLDLLAAHPYNTHHHRGLRVTSSTGSGSEAVAE WVLMNTMFLTRRMGAALRNQAGREWAPRALTGFRTISQLSVGIVGFGSIG RHVAERFLALGARKVTAVNTTGPPLSSSSSSSPCGYSRLGEVTVLPLLQR GGDGKPEARGGGGDDDDEKDGLREFLRDQDVLVLAAPLTPETRGLIGGAE LAALPLGAVVLNVARGPLLDERALAERLRSGHLAGAAIDVADQEPLDAAS PLWDVPNLVITPHVSAFHSKYNQNMLAIFEHNLRAHLCHRPVTEMRNVVQ LPVPSEPSPLGSKSNAAPKRPTKTAYAVKESSSKN

Polyethylene glycol (PEG) (Millipore Sigma, Burlington, Mass.) may also be used to enhance ligation. The examples show that PEG having a molecular weight in the range of 600-6000 enhances DNA assemble. For example, PEG MW may be selected from 500, 600, 800, 1000, 1500, 2000, 2500, 3000, 3500, 4000, 4500, 5000, 5500, 6000, 6500, 7000, 7500, 8000, 8500, 9000 and 10,000. Example 7 shows results with PEG 600, PEG 3350 and PEG 6000 at 6.8% w/v.

The user can input any of or all these factors into an interface to enable the computer to provide an effective set of overhangs for assembling target polynucleotides either from polynucleotide fragments defined by the user or from a complete polynucleotide sequence in put by the user. The effective set may vary from one computation to the next, but should exceed a defined threshold for fidelity, efficiency and/or yield of the target assembled polynucleotide (as described above, the ligation fidelity of a set of overhangs is the product of multiplying together the ligation fidelity of a single overhang). The calculated threshold for fidelity may be greater than 85%, 90%, 95%, 96%, 97%, 98% or 99%. It is desirable that the calculated fidelity of joining for a set of overhangs should exceed 95%. The actual fidelity can be established by selecting randomly 2-3 bacterial colonies on a culture plate and analyzing the inserts. The assembly fidelity percentage determined biochemically should preferably provide an approximately 95% probability (typically less than 15% variation) that the clone will have a correct assembly (with no mistakes).

The results shown in Tables 3-6 were obtained from biochemistry and sequencing analysis using methods described in the examples. It is envisaged that tables may be similarly constructed for rNMPs or a mixture rNMPs and dNMPs or modified nucleotides in a single overhang or for the overhang and its complement. In these circumstances a ligase other than T4 DNA ligase may be selected according to the known properties of ligation of generally available ligases. In other embodiments, a matrix with 3′ overhang on one axis and 3′ and 4′ overhang on the second axis may be used where the gap may be filled by the ligase or other gap filling enzyme using an dNTP, an rNTP and/or a labeled nucleotide such as a modified nucleotide such as a methylated nucleotide, a fluorescent nucleotide or a biotinylated nucleotide or other affinity binding domain. One or more of the overhangs pairs may be selected to have one fragment with a 3-nucleotide overhang and the other fragment to have a 4-nucleotide overhang. Where the gap is adjacent to the 3′ end of the double stranded DNA on the overhang, T4 DNA ligase can gap fill with the desired modified nucleotide. In this way the assembled molecule may be labeled at one or multiple sites suitable for visualization and/or immobilization for purposes of enrichment and the like.

Embodiments of the present methods enable the user to mix and match large or small numbers of fragments with overhangs with a range of sizes and types for scarless and/or sequence-modified junctions.

Embodiments of the method are suitable for identifying fidelity profiles and mismatch preferences for a variety of ligases that differ in regard to these features from T4 DNA ligase. In this way, ligation pairs that are low fidelity with T4 DNA ligase may be high fidelity for other ligases expanding the repertoire of optimized sets of overhangs.

Embodiments of the method and the data tables provided herein relating to fidelity and bias of cohesive end-joining provides the means to execute high-fidelity ligation such as required in applications that include the ligase chain reaction, generation of libraries for NGS sequencing including choice of adapters and related ligation-dependent methods for detecting specific DNA sequences.

TABLE 1 High- Deletion- Failure- Low- fidelity prone prone fidelity Junction Set Set Set Set 1 AAGG

GCCC 1′ TTCC CGGG 2 ACTC

GCCA 2′ TGAG CGGT 3 AGGA

ACCC 3′ TCCT TGGG 4 AGTC

AGCC 4′ TCAG TCGG 5 ATCA

AGCC 5′ TAGT TTCC 6 GCCG

CGCC 6′ CGGC GCGG 7 CTGA GCTG TAAA AGCG 7′ GACT CGAC ATTT TCGC 8 GCGA

CGGC 8′ CGCT GCCG 9 GGAA

AGGC 9′ TCCTT TCCG ¹A notation of

 indicates the junction pair used is identical to the HF set.

Implementation of Nucleic Acid Assembly Using a Computer Program and a General-Purpose Computer System

The various components of the various systems described herein may be implemented as a computer program using general-purpose computer systems. Such a computer system typically includes a main unit connected to both an output device that displays information to a user and an input device that receives input from a user. The main unit generally includes a processor connected to a memory system via an interconnection mechanism. The input device and output device also are connected to the processor and memory system via the interconnection mechanism.

One or more output devices may be connected to the computer system. Example output devices include, but are not limited to, liquid crystal displays (LCD), plasma displays, cathode ray tubes, video projection systems and other video output devices, printers, devices for communicating over a low or high bandwidth network, including network interface devices, cable modems, and storage devices such as disk or tape. One or more input devices may be connected to the computer system. Example input devices include, but are not limited to, a keyboard, keypad, track ball, mouse, pen and tablet, touchscreen, camera, communication device, and data input devices. The invention is not limited to the particular input or output devices used in combination with the computer system or to those described herein.

The computer system may be a general-purpose computer system, which is programmable using a computer programming language, a scripting language or even assembly language. The computer system may also be specially programmed, special purpose hardware. In a general-purpose computer system, the processor is typically a commercially available processor. The general-purpose computer also typically has an operating system, which controls the execution of other computer programs and provides scheduling, debugging, input/output control, accounting, compilation, storage assignment, data management and memory management, and communication control and related services. The computer system may be connected to a local network and/or to a wide area network, such as the Internet. The connected network may transfer to and from the computer system program instructions for execution on the computer, media data such as video data, still image data, or audio data, metadata, review and approval information for a media composition, media annotations, and other data.

A memory system typically includes a computer readable medium. The medium may be volatile or nonvolatile, writeable or non-writeable, and/or rewriteable or not rewriteable. A memory system typically stores data in binary form. Such data may define an application program to be executed by the microprocessor, or information stored on the disk to be processed by the application program. The invention is not limited to a particular memory system. Time-based media may be stored on and input from magnetic, optical, or solid-state drives, which may include an array of local or network attached disks.

System such as those described herein may be implemented in software, hardware, firmware, or a combination of the three. The various elements of the systems, either individually or in combination may be implemented as one or more computer program products in which computer program instructions are stored on a computer readable medium for execution by a computer or transferred to a computer system via a connected local area or wide area network. Various steps of a process may be performed by a computer executing such computer program instructions. The computer system may be a multiprocessor computer system or may include multiple computers connected over a computer network. The components described herein may be separate modules of a computer program, or may be separate computer programs, which may be operable on separate computers. The data produced by these components may be stored in a memory storage system or transmitted between computer systems by means of various communication media such as carrier signals.

All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference.

EMBODIMENTS

The following embodiments describe aspects of the methods described herein. These aspects include computer implemented methods and uses thereof.

Embodiment 1. A synthetic self-complementary oligonucleotide that comprises a double-stranded region and a loop, wherein the double-stranded region contains a binding sequence for PaqCl and wherein the oligonucleotide comprises unligatable 3′ and 5′ ends and cannot be cleaved by PaqCl.

In other words, the oligonucleotide forms a hairpin, where the stem of the hairpin is double-stranded and the loop is single-stranded. The double-stranded region may be 10-50 base pairs in length, e.g., 10-30 base pairs in length e.g., 15-30 bases. The oligonucleotide is capable of being bound by PaqCl via the binding sequence, but not cleaved. The oligonucleotide cannot be cleaved by PaqCl, meaning that the double stranded part of the oligonucleotide is not long enough to be cleaved by PaqCl. Specifically, the double-stranded region of the oligonucleotide may terminate 1-4 base pairs away from the binding site so that that there are no correctly-positioned phosphodiester bonds in a double-stranded region for the enzyme to cleave. Alternatively, the oligonucleotide may contain an uncleavable linkage at that would usually be cleaved. The 5′ and 3′ ends of the oligonucleotide may be flush or recessed by 1, 2, 3, 4, 5, 6, or more nucleotides, where either the 3′ end or the 5′ end can be recessed. The loop of the oligonucleotide is not critical and may be 4-20 nucleotides in some cases. Unligatable 3′ and 5′ ends are ends that cannot be ligated to another substrate by T4 DNA ligase in a ligation buffer. An unligatable 3′ end does not contain a 3′ hydroxyl. An unligatable 5′ end does not contain a 5′ phosphate. The unligatable ends prevent the oligonucleotide from participating in downstream ligation reactions. A 3′ end that contains a 3′ phosphate and a 5′ end that contains a C3 spacer are examples of unligatable ends.

Embodiment 2. The oligonucleotide of embodiment 1, wherein the double-stranded region is 10-50 or 10-30 base pairs in length.

Embodiment 3. The oligonucleotide of any of embodiments 1-2, wherein the oligonucleotide is less than 110 nucleotides or less than 100 nucleotides in length.

Embodiment 4. The oligonucleotide of any of embodiments 1-3, wherein the 3′ end of the oligonucleotide does not contain a 3′ hydroxyl.

Embodiment 5. The oligonucleotide of any of embodiments 1-4, wherein the 5′ end of the oligonucleotide is not a 5′ phosphate.

Embodiment 6. The oligonucleotide of any of embodiments 1-5, wherein the binding sequence is CACCTGC.

Embodiment 7. A reaction mixture comprising:

(a) a synthetic self-complementary oligonucleotide of any of embodiments 1-6; and

(b) PaqCl or a variant thereof having an amino acid sequence that has at least 90% amino acid sequence identity with SEQ ID NO:26.

In these embodiments, the amino acid sequence of the variant of PaqCl may be at least 92%, at least 95%, at least 98%, or at least 99% identical to SEQ ID NO:26, and it should have the same basic functional characteristics of PaqCl, i.e., it should be able to the binding site of PaqCl (CACCTGC) and make a double-stranded break a few bases away from the binding site to produce a four base overhang.

Embodiment 8. The reaction mixture of embodiment 7, further comprising a double-stranded DNA substrate for PaqCl, wherein the substrate contains a binding sequence for PaqCl and can be cleaved by PaqCl to produce a 4 base overhang.

Embodiment 9. The reaction mixture according to embodiment 8, wherein the binding sequence in the DNA substrate is CACCTGC.

Embodiment 10. The reaction mixture of any of embodiments 7-9, further comprising a phage derived ligase.

Embodiment 11. The reaction mixture according to any of embodiments 7-10, further comprising a plurality of DNA substrates having a binding site for PaqCl, wherein cleavage of the DNA substrates by PaqCl or a variant thereof produces a plurality of fragments that have compatible overhangs that can be ligated into a single molecule.

Embodiment 12. The reaction mixture of embodiment 11, further comprising a ligase.

Embodiment 13. The reaction mixture of embodiment 11 or 12, wherein the reaction mixture comprises at least 20 DNA substrates containing the binding site for PaqCl.

Embodiment 14. The reaction mixture of any of embodiments 12 and 13, wherein the ratio of the PaqCl or variant to ligase is 2.5-20 units of PaqCl or variant to 200-800 units of ligase.

It is within the scope of these embodiments to utilize a mixture of PaqCl and one or more variants of PaqCl in the same reaction mixture. This scope is intended when PaqCl or PaqCl or a variant thereof is described in any of the present embodiments above or below.

Embodiment 15. A method comprising:

(a) combining:

-   -   i. a synthetic self-complementary oligonucleotide of any of         embodiments 1-6;     -   ii. PaqCl or a variant thereof having an amino acid sequence         that has at least 90% amino acid sequence identity with SEQ ID         NO:26;     -   iii. a plurality of DNA substrates for PaqCl, wherein cleavage         of the DNA substrates by PaqCl or a variant thereof produces a         plurality of fragments that have compatible overhangs that can         be ligated into a single molecule; and     -   iv. a ligase, to produce a reaction mix; and

(b) incubating the reaction mix to produce a reaction product that comprises a DNA molecule that comprises sequence from the plurality of fragments.

Embodiment 16. The method of embodiment 15, further comprising transforming cells with the reaction product.

Embodiment 17. The method of embodiment 15 or 16, wherein the reaction mix further comprises a vector backbone.

Embodiment 18. The method of any of embodiments 15-17, wherein the reaction mix further comprises a DNA repair enzyme, a deadenylase, a crowding agent and/or the incubating is done by thermocycling.

Embodiment 19. The method of embodiment 18, wherein the reaction mix comprises polyethylene glycol (PEG) having a molecular weight in the range of 600-8000.

Embodiment 20. The method of embodiment 18, wherein the deadenylase is a yeast deadenylase.

Embodiment 21. The method of embodiment 18, wherein the DNA repair enzyme is EndoMS.

Embodiment 22. The method according to embodiment 20, wherein the plurality of DNA substrates is at least 20 plurality of DNA substrates.

Embodiment 23. The method according to embodiment 22, wherein the plurality of DNA substrates is at least 50 DNA substrates.

Embodiment 24. A kit for use in synthesizing a DNA from component sequences that are either contained in oligonucleotide fragments, cDNA or in genomic DNA, wherein the kit comprises: a type IIS restriction endonuclease having at least 90% (e.g., at least 95%, 98% or 99%) sequence identity to SEQ ID NO:26, a ligase, and optionally an additive selected from the group consisting of a deadenylase and a crowding agent.

Embodiment 25. The kit according to embodiment 24, wherein the Type IIS restriction endonuclease and the ligase are combined in a single container.

Embodiment 26. The kit according to embodiment 24, wherein the Type IIS restriction endonuclease and the ligase are in separate containers.

Embodiment 27. The kit according to any of embodiments 24-26, further comprises synthetic self-complementary oligonucleotide that comprises a double-stranded region and a loop, wherein the double-stranded region contains a binding sequence for PaqCl and wherein the oligonucleotide cannot be cleaved by PaqCl and comprises unligatable 3′ and 5′ ends.

Embodiment 28. The kit according to any of embodiments 24-27 wherein the kit contains a deadenylase that has at least 90% (e.g., at least 95%, 98% or 99%) sequence identity to any of SEQ ID NO:18-25.

Embodiment 29. The kit according to any of embodiments 24-28, wherein the crowding agent is polyethylene glycol (PEG).

Embodiment 30. The kit according to embodiment 29, wherein the PEG has a molecular weight in the range of 600-8000.

Embodiment 31. The kit according to any of embodiments 24-30, wherein the kit further comprises a mismatch specific endonuclease.

Embodiment 32. The kit according to any of embodiments 24-31 wherein the mismatch endonuclease is EndoMS.

Embodiment 33. The kit according to any of embodiments 24-32, further comprising in the same or separate container, one or more destination vectors.

Embodiment 34. The kit according to any of embodiments 24-33, wherein the kit further comprises competent prokaryotic or eukaryotic cells for receiving the destination vector.

All publications, patents, and patent applications mentioned in this specification are herein incorporated by reference to the same extent as if each individual publication, patent or patent application was specifically and individually indicated to be incorporated by reference including: U.S. application Ser. No. 17/286,066 filed Apr. 16, 2021; U.S. Provisional Application No. 63/125,530, filed Dec. 15, 2020; U.S. Provisional Application No. 63/213,807, filed Jun. 23, 2021; and U.S. Provisional Application No. 63/213,859, filed Jun. 23, 2021.

EXAMPLES

All enzymes and buffers were obtained from New England Biolabs, Ipswich, Mass. unless otherwise noted.

Example 1: Sequencing of Junction Regions Formed by Ligation of Overhangs

A single-molecule, next-generation sequencing assay was used to probe the fidelity of DNA ligase end-joining, from a mixed population of single stranded DNA overhangs. The assay utilized SMRT sequencing. Hairpin substrates incorporated the SMRTbell® (Pacific Biosciences, Menlo Park, Calif.) adapter and a short 2-base, 3-base, 4-base or 5-base 5′-overhang. The results of the analysis are shown in Tables 3-6. The method for obtaining the results are provided below for 3-base overhangs but the same approach was used to determine the 2-base, 4-base and 5-base overhangs. In place of Sapl which is a Type IIS restriction endonuclease that creates 3-base overhangs, restriction endonucleases that produced 2-base, 4-base and 5-base overhangs were used and recognition sites to permit cleavage by the restriction endonucleases were utilized in the section on preparation of substrates for multiplexed ligation fidelity and bias profiling assay. Examples of restriction endonucleases: 2-base cutters

For 3-base overhangs, the overhang region was randomized such that it contained all possible 3-base overhangs in approximately equal proportion. Ligation of these randomized pools created libraries with SMRTbell adapters on both ends and an insert region generated from the ligation of two overhangs. SMRT sequencing of the ligated libraries allowed direct read out of both overhangs from single ligation products. Systematic profiling of ligation events for all possible overhangs in a single experiment was achieved. The frequency of each product was assumed to be proportional to the efficiency of that particular end-joining reaction. This method was used to characterize the ligation of 3-base and 4-base overhangs by T4 DNA ligase under typical reaction conditions, allowing the comprehensive evaluation of the fidelity and bias of the reaction. The results are shown in Table 3.

Preparation of Substrates for Multiplexed Ligation Fidelity and Bias Profiling Assay

Initial PAGE-purified substrate precursor oligonucleotide was obtained from IDT (Coralville, Iowa). The sequence (Table 2) contained a 5′-terminal region, a randomized 3-base region, a Sapl binding site, a constant region, an internal 6-base randomized region as a control for synthesis bias, and a region corresponding to the SMRTbell sequencing adapter for SMRT sequencing. The oligonucleotide was designed with a short (7-base) complementary region such that they formed a primer-template junction hairpin structure. The precursor oligonucleotide was combined with Klenow Fragment (3′ 5′ exo-), yeast inorganic pyrophosphatase and dNTPs and an extension reaction performed.

The extended DNA was cut using Sapl to generate a 3-base overhang. Final concentration and extent of cutting was determined by Agilent Bioanalyzer® DNA 1000 (Agilent, Santa Clara, Calif.) and confirmed to be >95% cut.

In a typical reaction, substrate was combined with wt T4 DNA ligase and the ligation yield was determined by Agilent Bioanalyzer DNA 1000. The ligated library was treated with exonuclease III and exonuclease VII in Standard Taq Polymerase buffer for a 60 minute incubation at 37° C.

Pacific Biosciences SMRT Sequencing

Ligated overhang substrates libraries were prepared for sequencing according to the Pacific Biosciences Binding Calculator Version 2.3.1.1 and the DNA/Polymerase Binding Kit P6 v2 using the standard protocol, no-DNA control complex. Libraries were sequenced on a Pacific Biosciences RSII, Inserts corresponding to the same strand were grouped together, and a consensus sequence of each strand was built with the Arrow algorithm using the ccs program from SMRT Link software.

Each consensus sequence represented the product of ligating multiple Golden Gate fragments into a single assembly such that the resulting consensus reads were comprised of long fragments separated by short regions corresponding to ligation junctions. The ten known 300 nucleotide fragments, their coordinates and mapping direction in each consensus read from assembly libraries were determined using BLAST software. This information was then used to tabulate the frequency of pairwise ligation events and overall composition of assemblies. A number of filtering steps were applied to ensure integrity of the derived data. Any 300-nucleotide fragment was required to map entirely from the first to the last nucleotide in the consensus read. Additionally, only two types of ligation junctions were expected to be seen in consensus reads: junctions of length 3 or 4 (for different length overhangs) corresponding to overhang ligation during assembly reaction and corresponding junction lengths of 6 or 8 nucleotides resulting from blunt ligation during SMRT library preparation workflow. Respective barcodes in the opposite strands were required to be complementary.

One nucleotide variation in length or mismatch was permitted for each junction type to account for possible errors in the sequencing reads. If any of above conditions were not met, the resulting consensus read was excluded from the analysis. When a blunt ligation junction was detected in the consensus read, the entire read was split apart at such junctions.

At least five sub-reads per strand were required to build a consensus reads from which fewer than five sub-reads per strand were found were discarded. Resulting consensus sequences were aligned to the respective insert reference sequences using BLASR aligner, and sequence fragments corresponding to overhangs and barcodes were extracted for each strand. Frequencies of all observed overhang pairs in ligation products were tabulated and used to derive results. For each multiplexed ligation profile library, the internal barcodes were characterized to assess the degree of sequence bias introduced by the oligonucleotide synthesis.

For each read, the barcode sequence was extracted, and the fraction of each base at each position determined. The reported values are for the barcode strand produced by the oligonucleotide synthesis; the complementary strand, inserted during the polymerase extension step, had the complementary ratios. The error was reported as the standard deviation of all six positions from all sequencing runs using a given substrate.

Results

The multiplexed ligation profile results for 3-base overhangs formed after an incubation time of 1 hour at 25° C. were assembled and reported in a tabular format in Table 3. The results for TNA overhangs under these conditions show greatly reduced ligation fidelity. While the majority of correctly base-paired ligation partners were observed in very similar overall frequency (FIG. 7B, below the horizontal line). At incubation temperatures of 25° C. and 37° C. it was established that the 4 TNA overhangs had notably reduced ligation fidelity compared to the average. The corresponding ANT overhangs, despite being expected to be present in the exact same proportion of the initial substrate pool, did not show a reduced incidence compared to the other overhangs in the set at these temperatures for the specified incubation time.

From this data, it was concluded that ligation fidelity of overhangs varies significantly with their sequence. The range of observed ligation fidelity as a function of overhang identity was broad, from overhangs with very few observed mismatch ligation events (e.g., AAA, ATA, CAA) to those where a very large fraction of observations (>40%) found a ligation partner with one or more base pair mismatches (e.g., GCC and GGC). Overall, there was a weak trend towards lower fidelity with higher G/C content. More specifically, for 3-base overhangs, 5′-GNN sequences were highly represented in the lowest-fidelity overhangs, with 5′-TNN over-represented in the highest fidelity group. Increasing temperature (37° C., FIGS. 7C and 7D) resulted in an overall suppression of mismatch ligation, with no significant change to the overall patterns: the Kendall rank correlation coefficient equaled 0.87 when compared with individual ligation fractions observed at 25° C. and 37° C. (only ligations with more than 10 counts per ligation event were considered).

Additionally, there was minimal effect on the identity of the mismatches observed. Mismatch rates at 37° C. were 2-fold lower than at 25° C. as measured by the fraction of mismatch ligations; mean mismatch ligation fraction per overhang was 2.53×10⁻³ and 1.29×10⁻³, respectively.

For most overhangs, even those of the lowest fidelity, the bulk of the mismatch ligation events were derived from pairing with only a few (typically 2-3) other overhangs (Table 3). For example, GGC was one of the lowest fidelity overhangs, with only 54% of observations showing it paired with its Watson-Crick partner, GCC. However, its mispairing events are dominated by GCT (43% of mismatch ligation events) and ACC (38% of mismatch ligation events). For CGT, 76% of ligations were with its Watson-Crick partner, with nearly all of the observed mismatch ligations coming from pairing with the overhang GCG (90% of mismatch ligation events). Importantly, the overwhelming majority (98%) of mismatch overhangs at 1 hour at 25° C. had a single-base mismatch; 2 and 3-base mismatches were 1.8% and <0.1%, respectively.

Very similar results were observed for 1 hour at 37° C. (1, 2 and 3-base mismatches were 97.6%, 2.2% and <0.2%, respectively). Thus, individual overhangs that exhibit low fidelity were not promiscuous; rather they tend to pair with only a few specific mismatched sequences.

Ligation Preference for Mismatches Varies by Position and Strand Sense and is Context-Sensitive

Analysis of the observed mismatch ligation events further allowed identification of the types of mismatches tolerated by the ligase, and the effect of position and structural context on ligation preferences. FIG. 6A-6F shows the observed frequency of ligated mispairs at the ‘edge’ position versus the middle’ position for 3-base overhangs at 25° C. and 37° C. As with the overall fidelity, increasing temperature had little effect on the specific mismatch pairings observed or their relative frequency to each other, simply reducing overall mismatch frequency relative to Watson-Crick paired products.

At the edge position of 3-base overhangs (N1:N3′, FIGS. 6A and 6C), mismatch ligation was dominated by G:T mispairs, which make up 52% of all observed N1:N3_ mismatches (mismatches at this position total 7.1% of all ligation events, with G:T mismatches at this position comprising 3.7% of all ligation events). Interestingly, this preference was only for 5′-G mispairs, GNN/TNN; the reciprocal TNN/GNN mismatch was not especially prevalent (3.7% and 0.3% of all observed ligations, respectively). The ligation of a GNN/TNN mispair was independently assayed and compared to the ligation of the reciprocal TNN/GNN mispair to confirm this observation. Indeed, the 5′-G mismatch ligated ˜80-fold faster than the 5′-T mismatch (FIG. 5A-5B). The preference for edge G:T mismatches accounted for the over-representation of GNN overhangs displaying low overall fidelity; a G:T simply ligated much faster than any other mispairing in this position. After G:T, several purine:purine (A:A, A:G, and G:A) and the other purine:pyrimidine (A:C, C:A, T:G) mismatches were observed, with pyrimidine: pyrimidine mismatches disfavored. Adenine displayed the same 5′ mismatch preference; the ANN/CNN mispairing was ˜40-fold more prevalent than the reciprocal CNN/ANN mispairing (1.3% and 0.03% of ligation events, respectively).

At the middle position of 3-base overhangs (N2:N2, FIGS. 6B and 6D), a lower overall frequency of mismatches was observed, ˜3-fold less common compared to the total frequency for mismatches at the edge position (7.1% and 2.3% for edge and middle mismatches, respectively). At the middle position, T:T mismatches were modestly favored, ˜2-3 times more prevalent than any other single mismatch, with C:T, T:C, G:T and T:G all present at similar frequencies (FIG. 5B) A:C, C:A, C:C and purine:purine mismatches.

The fidelity of 4-base overhang ligation shared much in common with 3-base overhangs. As in the case of 3-base overhangs, G:T mismatches were highly favored, along with lesser amounts of T:T, purine:purine, and A:C mismatches. However, here, very similar profiles were seen at the edge and middle positions, in contrast to 3-base overhangs in which mismatches were dramatically dis-favored at the middle position, and only T:T mismatches were observed. Four-base overhangs also lack the dramatic asymmetry in preference for 5′-purines; while G:T is favored modestly over T:G (T in the template vs G in the template), it falls far short of the 10-fold preference observed for 3-base overhangs. Thus, the data is suggestive of a stronger influence of annealing on the mismatch preferences as compared to 3-base overhangs. However, the influence of ligase preference was still clear, with higher mismatch frequencies at the edge position and sequence dependence of mismatch prevalence. For example, cases of an edge mismatch with two GC and one AT base pair where both GCs are in the middle (N2:N3′ and N3:N2′) positions outnumber by a factor of two those where only one of the middle pairs is a GC. The fidelity of 2-base overhangs is very high while there is more variability in fidelity for the longer 5-base overhangs.

Further details for the analysis of 3-base and 4-base overhangs can be found in Potapov, et al. Nucleic Acid Research, 46, e79 (2018) and Potapov, et al. Cold Spring Harbor Laboratory, bioRxiv, doi: https://doi.org/10.1101/322297 (2018), incorporated by reference.

TABLE 2 Precursor and substrate sequences Substrate Sequence^(a) Ligation TCAGGTNNNCGAAGAGCTGCGATCCAGTGCGCCGTGCATT library GATCAACGCAANNNNNNATCTCTCTCTTTTCCTCCTCCTC precursor CGTTGTTGTTGTTGAGAGAG (SEQ ID NO: 1) Ligation pNNNCGAAGAGCTGCGATCCAGTGCGCCGTGCATTGATCA library ACGCAANNNNNNATCTCTCTCTTTTCCTCCTCCTCCGTTG substrate TTGTTGTTGAGAGAGATNNNNNNTTGCGTTGATCAATGCA CGGCGCACTGGATCGCAGCTCTTCG (SEQ ID NO: 2) Expected NNNNNNTTGCGTTGATCAATGCACGGCGCACTGGATCGCA insert^(b) GCTCTTCGNNNCGAAGAGCTGCGATCCAGTGCGCCGTGCA TTGATCAACGCAANNNNNN (SEQ ID NO: 3) ^(a)The Sapl (Type IIS restriction enzyme) binding site is indicated in bold. SMRT adapter region is underlined. ^(b)The expected insert length in 99 nt. The location of 3-base overhang is in position 49 . . . 51, 31-randomized region is in position 1 . . . 6, and 51-randomized region is position 94 . . . 99.

TABLE 3 Ligation fidelity for 3-base overhangs (18 hours at 25° C.). Correct, ×10⁻⁵ Mismatch, ×10⁻⁵ Fidelity, %^(a) Overhang Value S.D. Value S.D. Value S.D. Mismatch overhangs^(b) AAA 1403.8 14.2 11.1 4.1 99.2 0.3 TTC (43%); ATT (12%); TGT (10%) TAA 209.0 10.8 2.9 1.9 98.6 0.9 GTA (36%); TTT (27%); TTG (18%) ATA 1472.5 11.9 24.9 3.1 98.3 0.2 AAT (44%); GAT (26%); TTT (13%) CAA 1658.4 0.2 30.0 8.0 98.2 0.5 GTG (54%); ATG (34%); TGG (2%) TTC 1608.3 29.6 34.2 2.5 97.9 0.2 GAG (42%); GAT (17%); AAA (14%) TTG 1658.4 0.2 36.3 7.4 97.9 0.4 CAG (46%); CAT (22%); CTA (9%) AGA 1440.7 7.9 32.4 18.9 97.8 1.3 GCT (24%); ACT (23%); TCA (16%) TAG 1491.6 12.2 35.3 0.3 97.7 0.0 CTG (55%); CTT (35%); CTC (5%) TTA 209.0 10.8 5.0 2.0 97.6 1.0 GAA (21%); AAA (21%); TAG (11%) TCA 617.9 1.1 16.2 4.2 97.4 0.6 AGA (31%); GGA (28%); TGG (11%) TCG 1531.7 10.1 41.9 9.0 97.3 0.6 CGG (68%); CGT (9%); AGA (6%) TGA 617.9 1.1 21.5 1.2 96.6 0.2 GCA (43%); ACA (31%); TCT (10%) ACA 1437.3 19.3 50.4 15.3 96.6 1.0 TGC (54%); TGG (16%); TGA (13%) CAG 1415.5 35.6 51.2 0.8 96.5 0.1 TTG (33%); ATG (19%); GTG (19%) TGG 1609.6 39.8 66.0 18.0 96.1 1.1 CCG (41%); CCT (20%); ACA (12%) TAT 1472.5 11.9 63.9 3.6 95.8 0.2 GTA (71%); ATG (17%); ATT (7%) TCC 1619.4 43.6 71.6 18.6 95.8 1.2 GGG (68%); GGT (14%); AGA (5%) TAC 1453.7 30.9 87.0 3.7 94.4 0.3 GTG (69%); GTT (26%); GTC (3%) CGA 1531.7 10.1 98.1 1.3 94.0 0.1 ACG (51%); GCG (41%); CCG (2%) CCG 1531.1 69.8 101.0 24.2 93.8 1.6 AGG (39%); TGG (27%); CTG (14%) TTT 1403.8 14.2 94.7 8.5 93.7 0.5 GAA (82%); AAG (4%); AGA (4%) CGG 1531.1 69.8 120.9 29.1 92.7 1.9 ACG (41%); TCG (24%); GCG (11%) CTA 1491.6 12.2 120.4 23.9 92.5 1.4 AAG (56%); GAG (32%); TTG (3%) TGC 1316.9 18.0 107.4 20.8 92.5 1.3 GCG (47%); ACA (25%); GCT (20%) TCT 1440.7 7.9 119.6 7.8 92.3 0.4 GGA (81%); AGG (13%); TGA (2%) GAA 1608.3 29.6 139.5 15.5 92.0 0.9 TTT (56%); GTC (27%); ATC (12%) CCA 1609.6 39.8 162.3 8.0 90.8 0.6 AGG (73%); GGG (23%); CGG (2%) CAC 1147.7 67.3 133.6 8.9 89.6 1.1 ATG (54%); GCG (17%); GTT (13%) ATG 1593.4 13.4 198.9 20.5 88.9 1.1 CAC (36%); CTT (33%); TAT (5%) CTG 1415.5 35.6 177.7 12.4 88.8 0.9 CTG (50%); AAG (12%); TAG (11%) TGT 1437.3 19.3 181.6 6.7 88.8 0.2 GCA (83%); ACG (11%); ACT (3%) ATT 1638.5 19.7 207.1 11.2 88.8 0.4 GAT (84%); AGT (4%); ATT (3%) AAT 1638.5 19.7 211.6 21.3 88.6 0.9 GTT (74%); ATC (16%); ATA (5%) AAG 1279.7 15.5 175.8 12.3 87.9 0.9 CTC (40%); CTA (38%); CTG (13%) ATC 1336.5 8.9 188.5 19.1 87.6 1.2 GAC (33%); AAT (17%); GGT (14%) AGT 1526.9 0.5 217.2 27.7 87.5 1.4 GCT (83%); ATT (4%); ACC (3%) CCC 1322.4 107.4 197.6 68.8 87.0 4.8 AGG (61%); GTG (20%); GAG (6%) GTA 1453.7 30.9 248.5 7.0 85.4 0.6 AAC (39%); GAC (31%); TAT (18%) CAT 1593.4 13.4 281.4 38.2 85.0 1.9 GTG (87%); ACG (3%); TTG (3%) AAC 1259.1 35.1 234.7 18.4 84.3 0.7 GTC (42%); GTA (41%); GTG (12%) GGA 1619.4 43.6 305.0 27.6 84.2 1.6 GCC (33%); TCT (32%); ACC (31%) ACT 1526.9 0.5 289.8 20.6 84.0 1.0 GGT (64%); AGC (24%); AGG (5%) GCA 1316.9 18.0 330.4 2.2 79.9 0.3 TGT (45%); AGC (33%); GGC (15%) CTC 1313.9 25.9 358.8 10.9 78.6 0.8 GTG (57%); AAG (19%); GCG (12%) AGG 1236.8 51.8 342.9 52.8 78.3 3.3 CCC (35%); CCA (35%); CCG (11%) CGT 1250.0 0.8 386.9 35.2 76.4 1.7 GCG (90%); GAG (2%); AGG (2%) CTT 1279.7 15.5 405.7 18.1 75.9 0.6 GAG (71%); ATG (16%); AGG (4%) GAG 1313.9 25.9 425.9 4.2 75.5 0.5 CTT (67%); CTA (9%); CTG (4%) CGC 1055.4 20.0 342.1 33.9 75.5 2.2 ACG (82%); GTG (5%); GCT (4%) CCT 1236.8 51.8 408.9 48.8 75.2 3.0 GGG (90%); TGG (3%); ATG (2%) ACG 1250.0 0.8 432.2 44.7 74.3 2.0 CGC (65%); CGA (12%); CGG (12%) AGC 950.7 21.1 337.8 13.5 73.8 1.2 GCA (32%); GCC (31%); ACT (20%) ACC 1258.3 110.3 498.5 58.2 71.6 4.1 GGC (57%); GGA (19%); GGG (14%) GAT 1336.5 8.9 533.5 16.6 71.5 0.8 GTC (59%); ATT (33%); ATG (1%) GGG 1322.4 107.4 608.8 90.4 68.5 4.9 CCT (61%); ACC (11%); TCC (8%) GTT 1259.1 35.1 603.3 20.1 67.6 1.3 GAC (55%); AAT (26%); ACC (4%) GGT 1258.3 110.3 623.4 97.8 66.9 5.4 GCC (60%); ACT (30%); ATC (4%) GCG 1055.4 20.0 564.8 33.5 65.1 1.8 CGT (61%); TGC (9%); CTC (7%) GAC 1061.5 2.1 570.1 36.7 65.1 1.4 GTT (58%); GTA (13%); ATC (11%) GTG 1147.7 67.3 679.6 48.1 62.8 3.0 CAT (36%); CTC (30%); TAC (9%) GCT 950.7 21.1 572.5 46.7 62.4 2.5 GGC (56%); AGT (32%); TGC (4%) GTC 1061.5 2.1 673.5 26.0 61.2 0.9 GAT (47%); AAC (15%); GTC (12%) GCC 864.7 68.8 730.8 98.5 54.2 5.4 GGT (51%); AGC (14%); GGA (14%) GGC 864.7 68.8 748.9 48.2 53.6 3.6 GCT (43%); ACC (38%); GCA (7%) Standard deviations were derived from two experimental replicates, while the values themselves were derived from the combined data. ^(a)Fidelity is calculated as the fraction of correct ligations divided by the total fraction of ligations for a given overhang. ^(b)Top 3 mismatch overhangs are given for each overhang. All overhangs are written in the 5′-to-3′ direction. The numbers in parenthesis give the percentage for the given mismatch ligation relative to the total number of mismatch ligations for the overhang.

TABLE 4 Ligation fidelity for 4-base overhangs (18 hours at 25° C.) Overhang Correct, ×10⁻⁵ Mismatch, ×10⁻⁵ Fidelity, % ¹ Mismatch Overhangs ² AAAA 264.3 1.6 99.4 TTTG (35%); CTTT (13%); TTAT (13%) AAGA 329.4 3.0 99.1 GCTT (14%); TTTT (12%); TCTG (12%) GAAA 378.3 5.0 98.7 TTTT (25%); TTCC (10%); ATTC (8%) ACAA 333.4 4.8 98.6 TTGG (45%); TTGC (13%); ATGT (7%) CAAA 310.8 4.7 98.5 GTTG (30%); ATTG (18%); CTTG (9%) ATAA 209.3 3.2 98.5 TAAT (17%); TTGT (15%); TTTT (13%) AATA 324.5 5.5 98.3 GATT (22%); TGTT (18%); AATT (10%) AGAA 354.4 6.2 98.3 TTGT (42%); TTCG (12%); TGCT (8%) AACA 380.9 7.1 98.2 GGTT (19%); TGTG (16%); TGTC (14%) ACGA 349.1 7.3 98.0 GCGT (17%); TCGG (16%); TTGT (14%) GTAA 350.6 8.1 97.7 TTAT (20%); TGAC (9%); TTGC (9%) CCAA 335.4 7.8 97.7 GTGG (23%); TGGG (12%); ATGG (12%) ACCA 363.5 9.3 97.5 TGGG (28%); GGGT (23%); TGGC (13%) CGAA 403.0 10.4 97.5 GTCG (25%); ATCG (15%); TTTG (13%) CTAA 296.9 8.8 97.1 GTAG (24%); TCAG (10%); TAAG (9%) ATGA 367.8 11.4 97.0 GCAT (24%); TTAT (20%); TCGT (13%) GCAA 355.4 11.2 96.9 TTGT (37%); TGGC (11%); TAGC (9%) AGGA 315.3 10.4 96.8 GCCT (32%); TTCT (14%); ACCT (8%) TCAA 194.2 6.7 96.7 TTGG (68%); TTGT (8%); TGGA (5%) GAGA 287.9 9.9 96.7 GCTC (24%); TCTT (18%); TTTC (11%) ATCA 360.0 13.3 96.4 GGAT (43%); AGAT (10%); CGAT (9%) ACTA 266.6 10.0 96.4 TGGT (39%); GAGT (26%); TTGT (8%) CAGA 381.8 14.4 96.4 GCTG (53%); ACTG (13%); TTTG (6%) TTTA 100.1 4.1 96.1 TAAG (49%); TAAT (10%); TTTA (7%) TAGA 210.1 8.8 96.0 TCTG (37%); TCTT (37%); GCTA (6%) TTCA 294.2 12.4 96.0 TGAG (60%); TGAT (12%); TGGA (8%) TTGA 194.2 8.8 95.7 TCAG (38%); TCAT (16%); GCAA (6%) TGAA 294.2 13.4 95.6 TTCG (44%); TTCT (25%); GTCA (7%) ATTA 314.9 14.4 95.6 GAAT (38%); TGAT (25%); AAAT (9%) AGTA 343.6 15.7 95.6 GACT (41%); TGCT (18%); CACT (8%) ATAT 369.5 17.9 95.4 GTAT (24%); TTAT (18%); AAAT (14%) TATA 187.8 9.3 95.3 TATG (40%); TATT (34%); TGTA (5%) GGAA 350.4 18.3 95.0 TTGC (25%); TTCT (17%); TTTC (16%) AAAC 369.8 20.1 94.8 GTTG (31%); GTTA (17%); GTTC (15%) TAAA 100.1 5.5 94.8 TTTT (39%); TTTG (35%); ATTA (5%) GATA 355.2 20.6 94.5 GATC (28%); TGTC (23%); TATT (12%) AACC 358.7 23.0 94.0 GGTG (18%); GGTC (15%); GGGT (14%) TTAT 209.3 13.8 93.8 ATAT (23%); ATAG (19%); ATGA (16%) TTTT 264.3 18.1 93.6 AAAG (37%); AAAT (22%); TAAA (12%) AATT 380.4 26.5 93.5 GATT (39%); TATT (38%); ATTT (4%) AAAG 329.5 23.3 93.4 TTTT (29%); CTTA (16%); CTTG (15%) CCCA 249.4 18.2 93.2 GGGG (51%); CGGG (14%); AGGG (11%) TTGT 333.4 25.1 93.0 ACAG (37%); GCAA (16%); ACAT (11%) AATC 320.8 24.4 92.9 GGTT (52%); GATC (7%); GTTT (6%) AAGC 326.7 25.2 92.9 GGTT (24%); GCTG (19%); GCTA (11%) TTAA 18.5 1.5 92.7 TTGA (14%); GTAA (14%); TTAG (14%) TTAC 350.6 27.9 92.6 GTAG (33%); GTGA (28%); GTAT (15%) CAAC 332.0 26.4 92.6 GGTG (35%); GTTT (11%); GATG (10%) TCTA 210.1 17.2 92.4 TAGG (80%); TAGT (4%); TGGA (3%) ATAG 357.8 29.9 92.3 CTTT (30%); CTGT (27%); TTAT (9%) ATCC 360.4 30.9 92.1 GGGT (44%); GGTT (8%); GGAC (7%) TACA 344.9 29.9 92.0 TGTG (48%); TGTT (38%); TGTC (3%) TTCT 354.4 31.3 91.9 AGAG (48%); AGAT (15%); TGAA (11%) TGTA 344.9 30.7 91.8 TACG (49%); TACT (21%); GACA (10%) TGGA 331.6 29.6 91.8 TCCG (49%); TCCT (25%); GCCA (4%) CCCC 189.1 17.1 91.7 GGTG (26%); TGGG (20%); AGGG (12%) TCGA 296.0 28.4 91.2 TCGG (85%); TCGT (4%); GCGG (1%) AAGT 277.4 26.8 91.2 GCTT (76%); TCTT (5%); AGTT (4%) ATAC 359.7 34.8 91.2 GGAT (34%); GTGT (26%); GTTT (10%) CTAT 357.8 34.7 91.2 GTAG (26%); TTAG (16%); ATTG (14%) CACA 344.0 34.6 90.9 GGTG (61%); TGGG (9%); TGCG (7%) TTAG 296.9 32.1 90.2 CTAG (31%); CTGA (23%); CTAT (17%) CATA 357.2 39.2 90.1 GATG (41%); TGTG (24%); AATG (9%) GACA 318.4 36.5 89.7 TGTT (26%); GGTC (26%); TGGC (14%) ACCC 302.0 34.7 89.7 GGGG (50%); GGGC (19%); GGGA (6%) AATG 355.0 40.9 89.7 TATT (47%); CATG (12%); CATA (9%) ATGT 353.9 41.3 89.5 GCAT (30%); AGAT (28%); TCAT (14%) ATTT 358.0 42.7 89.3 TAAT (44%); GAAT (29%); AGAT (10%) TATT 324.5 40.0 89.0 AATG (49%); AATT (25%); TATA (8%) CCGA 297.4 36.7 89.0 GCGG (41%); TTGG (28%); ACGG (11%) AGCA 254.5 31.8 88.9 TGGT (34%); GGCT (22%); TGCG (8%) TTTC 378.3 47.5 88.9 GAAG (56%); GAAT (22%); GGAA (6%) CAGT 226.9 30.4 88.2 GCTG (65%); TCTG (11%); AGTG (11%) ACTT 277.4 37.2 88.2 TAGT (41%); GAGT (26%); AGGT (10%) CAAG 326.0 43.9 88.1 TTTG (58%); GTTG (8%); CTTT (6%) CGGA 354.7 49.1 87.9 GCCG (51%); TTCG (20%); ACCG (6%) GTAT 359.7 50.2 87.7 GTAC (33%); ATGC (14%); AGAC (9%) TCTT 329.4 46.2 87.7 AAGG (77%); TAGA (7%); GAGA (4%) CTTA 319.4 45.2 87.6 GAAG (34%); TGAG (24%); TTAG (10%) TCCA 331.6 47.2 87.5 TGGG (85%); TGGT (7%); GGGA (2%) TTTG 310.8 45.4 87.3 CAAG (56%); CAAT (14%); CATA (6%) CTCA 329.4 48.2 87.2 GGAG (47%); TGTG (14%); CGAG (11%) CCTA 261.5 38.4 87.2 GAGG (29%); TGGG (28%); ATGG (9%) AAAT 358.0 53.8 86.9 GTTT (73%); TTTT (7%); ATTG (6%) ATTC 356.1 54.1 86.8 GGAT (59%); GAGT (8%); TAAT (7%) CGTA 359.3 55.5 86.6 GACG (39%); TGCG (22%); AACG (15%) CACC 297.0 46.0 86.6 GGGG (31%); GGCG (20%); GGTT (8%) CTGA 337.7 52.4 86.6 GCAG (50%); TTAG (14%); TCTG (9%) CCAG 319.9 50.3 86.4 TTGG (52%); ATGG (11%); CGGG (7%) CAAT 367.9 58.1 86.4 GTTG (76%); TTTG (11%); ATCG (2%) ATCT 367.4 58.2 86.3 TGAT (58%); GGAT (28%); AGGT (3%) AGTT 348.3 55.5 86.3 TACT (47%); GACT (30%); AGCT (7%) ACGT 303.1 50.2 85.8 GCGT (58%); AGGT (8%); ACGG (8%) TTCC 350.4 58.1 85.8 GGAG (57%); GGAT (20%); GGGA (10%) CTAG 316.0 53.1 85.6 CTTG (29%); CTGG (25%); TTAG (19%) TAAG 319.4 54.0 85.5 CTTT (41%); CTTG (41%); CTTC (6%) CAGC 308.8 53.4 85.2 GGTG (37%); GTTG (16%); ACTG (10%) GCTA 318.1 55.9 85.0 GAGC (30%); TAGT (25%); TGGC (20%) CCAC 267.0 47.7 84.9 GGGG (59%); GCGG (13%); GAGG (10%) TTCG 403.0 72.4 84.8 CGAG (56%); CGGA (13%); CGAT (12%) CCAT 312.2 56.4 84.7 GTGG (68%); TTGG (13%); AGGG (8%) TTGG 335.4 61.6 84.5 CCAG (43%); CCGA (17%); CCAT (12%) ATTG 367.9 70.5 83.9 TAAT (41%); CGAT (20%); CATT (13%) ACGC 293.0 57.8 83.5 GCGG (29%); GGGT (20%); GCGC (16%) ACCT 319.2 63.5 83.4 TGGT (44%); GGGT (32%); AGGG (10%) TTGC 355.4 70.9 83.4 GCAG (56%); GCAT (13%); GCGA (12%) AGTC 300.5 60.2 83.3 GGCT (52%); GATT (12%); GAGT (6%) TAGT 266.6 53.7 83.2 ACTG (35%); ACTT (28%); GCTA (26%) TCAG 337.7 68.2 83.2 CTGG (69%); CTGT (17%); TTGA (5%) GTTA 323.6 66.2 83.0 GAAC (32%); TAAT (29%); TGAC (15%) AACT 348.3 72.3 82.8 GGTT (54%); TGTT (31%); AGTC (3%) ATGC 339.1 71.4 82.6 GCGT (33%); GGAT (28%); GTAT (10%) AAGG 255.1 55.0 82.3 TCTT (64%); CCTG (9%); CGTT (5%) CGCA 254.3 55.7 82.0 GGCG (42%); CGCG (14%); AGCG (12%) TCTG 381.8 83.7 82.0 CAGG (75%); CTGA (6%); CAGT (4%) GCGA 281.7 61.8 82.0 TCGT (58%); TTGC (14%); GCGC (9%) ACAT 353.9 77.8 82.0 GTGT (70%); ATGG (14%); ATGC (5%) TCAT 367.8 82.8 81.6 ATGG (46%); GTGA (41%); ATGT (7%) ACAG 322.4 73.8 81.4 CTGG (60%); CTGC (13%); TTGT (13%) GGGA 254.2 58.5 81.3 TCCT (30%); GCCC (29%); TTCC (10%) ACAC 303.8 70.0 81.3 GTGG (59%); GTGC (16%); GGGT (9%) TATC 355.2 82.7 81.1 GATG (56%); GATT (29%); GGTA (5%) CTAC 285.7 67.4 80.9 GGAG (37%); GTTG (23%); GTGG (18%) TATG 357.2 84.8 80.8 CATG (52%); CATT (29%); CATC (6%) TGCA 347.9 83.5 80.6 TGCG (66%); TGCT (21%); GGCA (5%) TAAT 314.9 75.9 80.6 ATTG (38%); GTTA (26%); ATTT (25%) ACTC 283.8 68.6 80.5 GGGT (59%); GAGG (17%); GAGC (7%) AGAG 274.0 67.4 80.3 TTCT (22%); CTGT (21%); CTCG (20%) GGTA 296.5 73.0 80.3 TACT (31%); GACC (29%); TGCC (13%) TACT 343.6 86.7 79.8 AGTT (30%); GGTA (26%); AGTG (25%) TCGT 349.1 88.6 79.8 ACGG (46%); GCGA (41%); ACGT (4%) GTGA 320.8 82.2 79.6 TCAT (41%); GCAC (33%); TTAC (10%) GTAG 285.7 75.5 79.1 CTGC (30%); CTTC (22%); TTAC (12%) AGTG 246.9 65.7 79.0 TACT (32%); CATT (13%); CACG (13%) TCAC 320.8 86.1 78.8 GTGG (71%); GTGT (20%); GGGA (2%) AGAT 367.4 98.7 78.8 GTCT (61%); ATGT (12%); ATCG (8%) AGGT 319.2 86.8 78.6 GCCT (57%); AGCT (15%); TCCT (7%) TCCT 315.3 86.2 78.5 AGGG (59%); GGGA (20%); TGGA (9%) TAAC 323.6 89.2 78.4 GTTG (47%); GTTT (40%); GTTC (9%) TGTT 380.9 107.2 78.0 AACG (50%); AACT (21%); TACA (11%) CATT 355.0 100.8 77.9 GATG (48%); TATG (24%); ATTG (9%) ATCG 324.1 92.2 77.9 TGAT (56%); CGGT (9%); CGAG (9%) CTTT 329.5 94.9 77.6 GAAG (37%); TAAG (24%); AGAG (11%) GTAC 345.4 102.5 77.1 GTGC (27%); GGAC (27%); GTAT (16%) CTCC 224.0 66.8 77.0 GGTG (49%); GGGG (21%); GGCG (14%) ATGG 312.2 94.0 76.9 TCAT (41%); ACAT (12%); CCGT (10%) AGAC 291.9 89.7 76.5 GTGT (30%); GTCG (21%); GTTT (20%) AACG 296.7 93.3 76.1 TGTT (57%); CGTG (10%); CGTA (9%) GATT 320.8 102.9 75.7 GATC (47%); TATC (23%); AATT (10%) TCTC 287.9 92.3 75.7 GAGG (78%); GAGT (9%); GGGA (6%) ACCG 313.0 100.7 75.7 CGGG (40%); TGGT (39%); CGGC (9%) TCCG 354.7 116.7 75.3 CGGG (66%); CGGT (16%); TGGA (12%) CCTT 255.1 84.2 75.2 GAGG (38%); TAGG (31%); AGGG (13%) CTTG 326.0 107.8 75.2 CGAG (32%); TAAG (20%); CTAG (14%) CTCG 302.2 99.9 75.2 TGAG (42%); CGGG (14%); AGAG (13%) TGAG 329.4 109.2 75.1 CTCG (39%); CTCT (33%); CTTA (10%) GAAC 308.7 102.7 75.0 GTTT (50%); GTTA (21%); GTAC (7%) CATG 359.9 119.9 75.0 TATG (37%); CGTG (29%); CTTG (12%) TAGC 318.1 106.5 74.9 GCTT (43%); GCTG (42%); GCTC (7%) TAGG 261.5 87.9 74.8 CCTG (39%); CCTT (30%); TCTA (16%) CTGT 322.4 110.3 74.5 GCAG (46%); ACTG (13%); AGAG (13%) GAGT 283.8 97.4 74.5 GCTC (64%); ACTT (10%); TCTC (9%) GAAT 356.1 122.2 74.4 GTTC (66%); ATTT (10%); TTTC (8%) CCGT 277.7 95.4 74.4 GCGG (54%); TCGG (16%); AGGG (12%) TACC 296.5 103.4 74.1 GGTG (48%); GGTT (40%); GGTC (6%) CATC 297.4 104.8 73.9 GGTG (63%); GTTG (16%); TATG (5%) CGAT 324.1 115.0 73.8 GTCG (62%); ATTG (12%); TTCG (8%) TACG 359.3 127.6 73.8 CGTG (43%); CGTT (29%); TGTA (12%) TCCC 254.2 90.5 73.8 GGGG (73%); GGGT (20%); GTGA (1%) CCCG 225.5 81.8 73.4 TGGG (72%); AGGG (12%); GGGG (5%) CGTT 296.7 109.9 73.0 GACG (37%); TACG (34%); AGCG (12%) GCCA 283.5 105.5 72.9 TGGT (78%); GGGC (11%); CGGC (3%) GAAG 270.0 101.4 72.7 CTTT (35%); TTTC (26%); CTTA (15%) CGAG 302.2 114.8 72.5 TTCG (35%); CTTG (30%); ATCG (7%) CCGC 224.1 87.0 72.0 GTGG (42%); ACGG (21%); GGGG (20%) GTCA 272.9 106.9 71.8 TGAT (53%); GGAC (27%); CGAC (4%) GATC 321.7 126.1 71.8 GATT (39%); GGTC (36%); GATA (5%) CTCT 274.0 109.2 71.5 GGAG (47%); TGAG (33%); AGTG (5%) AGGC 233.5 93.5 71.4 GGCT (25%); GCTT (16%); GCGT (13%) TCGC 281.7 116.0 70.8 GCGG (79%); GCGT (12%); GGGA (1%) CTTC 270.0 113.9 70.3 GGAG (51%); GTAG (15%); GATG (10%) CCCT 189.6 80.4 70.2 TGGG (48%); GGGG (43%); CGGG (2%) CCTG 278.5 120.8 69.7 CGGG (37%); TAGG (29%); CTGG (15%) GAGC 270.2 117.7 69.7 GCTT (43%); GCTA (14%); GGTC (13%) CACG 299.6 131.7 69.5 TGTG (59%); CGGG (9%); AGTG (6%) CCTC 202.3 90.0 69.2 GGGG (59%); GTGG (18%); GCGG (7%) ACGG 277.7 123.5 69.2 TCGT (33%); CCGG (30%); CCGC (15%) TGAT 360.0 160.4 69.2 GTCA (35%); ATCG (32%); ATCT (21%) GTTT 369.8 165.9 69.0 GAAC (31%); AAAT (24%); TAAC (21%) TCGG 297.4 133.8 69.0 CCGG (61%); TCGA (18%); CCGT (12%) GCTT 326.7 147.0 69.0 GAGC (34%); TAGC (31%); AAGT (14%) GCAT 339.1 153.2 68.9 GTGC (73%); ATGT (8%); TTGC (6%) CAGG 278.5 127.0 68.7 TCTG (49%); ACTG (34%); CGTG (4%) AGCC 240.7 110.9 68.5 GGGT (34%); GGTT (18%); GGCG (11%) CGAC 244.9 116.4 67.8 GTTG (45%); GGCG (25%); GACG (5%) ACTG 226.9 112.8 66.8 CAGG (38%); CGGT (20%); TAGT (17%) AGCT 273.2 136.5 66.7 GGCT (42%); TGCT (27%); AGGT (9%) CTGG 319.9 160.0 66.7 TCAG (30%); ACAG (27%); CCGG (12%) TGTC 318.4 160.2 66.5 GACG (47%); GACT (32%); GGCA (11%) TGGT 363.5 184.8 66.3 GCCA (44%); ACCG (21%); ACCT (15%) TGTG 344.0 176.1 66.1 CACG (44%); CACT (26%); TACA (8%) CGGT 313.0 163.6 65.7 GCCG (44%); AGCG (19%); ACTG (14%) CTGC 241.1 126.1 65.7 GCTG (26%); GCGG (20%); GGAG (18%) CACT 246.9 129.3 65.6 GGTG (49%); TGTG (36%); AGCG (5%) CGTC 262.8 139.1 65.4 GGCG (42%); GATG (19%); GAGG (11%) GGTT 358.7 205.8 63.5 GACC (33%); TACC (20%); AACT (19%) CGTG 299.6 172.3 63.5 TACG (32%); CATG (20%); CGCG (19%) GCAG 241.1 141.9 63.0 CTGT (36%); TTGC (28%); CTGA (18%) GATG 297.4 175.1 62.9 CATT (27%); TATC (26%); CGTC (15%) CCGG 268.6 158.5 62.9 TCGG (51%); ACGG (24%); CTGG (12%) GACT 300.5 178.2 62.8 GGTC (43%); TGTC (29%); AGTT (9%) GCTG 308.8 183.6 62.7 CGGC (27%); TAGC (24%); CTGC (18%) GCTC 270.2 163.6 62.3 GGGC (39%); GAGT (38%); GTGC (6%) GTGT 303.8 185.9 62.0 GCAC (31%); ACAT (29%); AGAC (14%) AGGG 189.6 116.7 61.9 TCCT (44%); CCGT (10%); CCTT (9%) TGAC 272.9 168.8 61.8 GTCG (45%); GTCT (35%); GTTA (6%) GCAC 236.0 148.4 61.4 GTGT (39%); GGGC (20%); GTGA (18%) GTTG 332.0 210.0 61.3 CGAC (25%); CAAT (21%); TAAC (20%) GACC 233.7 149.0 61.1 GGTT (46%); GGGC (15%); GGTA (14%) GTTC 308.7 199.1 60.8 GAAT (41%); GGAC (35%); GTAC (5%) GCGT 293.0 190.2 60.6 GCGC (49%); ACGT (15%); ATGC (13%) GGAT 360.4 244.3 59.6 GTCC (52%); ATTC (13%); ATGC (8%) CGCT 223.3 154.5 59.1 GGCG (42%); TGCG (38%); AGTG (5%) GTCT 291.9 205.8 58.7 AGAT (29%); TGAC (29%); GGAC (26%) TGGG 249.4 178.0 58.4 CCCG (33%); TCCA (23%); CCCT (22%) TGGC 283.5 203.0 58.3 GCCG (41%); GCCT (31%); GGCA (11%) GGCA 229.0 168.5 57.6 TGCT (37%); GGCC (16%); TGGC (13%) CGCC 189.1 140.9 57.3 GGTG (34%); GGGG (19%); GTCG (8%) CGGC 225.2 173.9 56.4 GCTG (29%); GTCG (21%); GGCG (21%) GACG 262.8 204.4 56.3 TGTC (37%); CGTT (20%); CGGC (11%) TGCC 229.0 185.3 55.3 GGCG (48%); GGCT (36%); GGTA (5%) GTCC 236.7 193.4 55.0 GGAT (66%); GGGC (13%); GGCC (6%) GAGG 202.3 167.4 54.7 TCTC (43%); CCTT (19%); CGTC (9%) TGCT 254.5 214.7 54.2 AGCG (36%); GGCA (29%); AGCT (17%) GCCC 209.7 179.3 53.9 GGGT (76%); GGGA (9%); GTGC (2%) GCCT 233.5 200.1 53.9 GGGC (33%); TGGC (32%); AGGT (25%) GCGC 208.5 180.7 53.6 GCGT (51%); GTGC (14%); GGGC (12%) GTGG 267.0 233.7 53.3 TCAC (26%); ACAC (18%); CCAT (16%) AGCG 223.3 205.6 52.1 TGCT (37%); CGCG (15%); CGGT (15%) CGGG 225.5 220.9 50.5 TCCG (35%); CCTG (20%); ACCG (18%) GCCG 225.2 220.9 50.5 TGGC (37%); CGGT (33%); CGGA (11%) GGTC 233.7 232.6 50.1 GACT (33%); GGCC (24%); GATC (20%) GGGT 302.0 303.7 49.9 GCCC (45%); ACTC (13%); AGCC (12%) TGCG 254.3 258.0 49.6 CGCG (40%); CGCT (23%); TGCA (21%) GTGC 236.0 239.5 49.6 GCAT (47%); GGAC (15%); GTAC (12%) GTCG 244.9 251.2 49.4 TGAC (30%); CGAT (28%); CGGC (14%) GGAG 224.0 234.9 48.8 CTTC (25%); CTCT (22%); TTCC (14%) GCGG 224.1 238.8 48.4 TCGC (38%); CCGT (21%); CTGC (10%) GGAC 236.7 262.7 47.4 GTTC (26%); GTCT (20%); GTGC (13%) GGTG 297.0 341.7 46.5 CATC (19%); CACT (19%); TACC (14%) CGCG 188.6 221.9 45.9 TGCG (46%); CGTG (15%); AGCG (14%) GGCT 240.7 318.5 43.0 GGCC (30%); TGCC (21%); AGCT (18%) GGGC 209.7 299.0 41.2 GCCT (22%); GCTC (21%); GGCC (14%) GGGG 189.1 294.4 39.1 TCCC (22%); CCTC (18%); CCCT (12%) GGCC 174.6 297.6 37.0 GGCT (33%); GGTC (19%); GGGC (14%) GGCG 189.1 358.8 34.5 TGCC (25%); CGCT (18%); CGTC (16%) ¹ Fidelity is calculated as the fraction of correct ligations divided by the total fraction of ligations for a given overhang. ² Top 3 mismatch overhangs are given for each overhang. All overhangs are written in the 5′-to-3′ direction. The numbers in parenthesis give the percentage for the given mismatch ligation relative to the total number of mismatch ligations for the overhang.

TABLE 5 Ligation fidelity for 2-base overhangs (16 hours at 25° C.). Although the number of combinations presented by two base overhangs is small with a maximum of 6 fragments in one pot, advantages include almost total freedom of where to break target sequence and virtually ensures the assembly products are error free. The Type IIS Btsl, with a preferred reaction temperature of 50° C. is an example of a restriction endonuclease that can generate a 2-base overhang. Overhang Correct, ×10⁻⁵ Mismatch, ×10⁻⁵ Fidelity, %¹ Mismatch Overhangs² AA 6375 6 99.9 TC (50%); TG (50%) AC 6400 10 99.9 GA (33%); TT (33%); AT (33%) AG 6579 22 99.7 GT (86%); AT (14%) AT 6406 10 99.9 AC (33%); AG (33%); CT (33%) CA 5100 13 99.8 CA (50%); TT (25%); GG (25%) CC 6100 3 99.9 CG (100%) CG 6068 19 99.7 CT (33%); GG (33%); CC (17%) CT 6579 13 99.8 CG (50%); GG (25%); AT (25%) GA 6745 13 99.8 GA (50%); AC (25%); GC (25%) GC 6630 19 99.7 GG (50%); GA (17%); CG (17%) GG 6100 26 99.6 GC (38%); CG (25%); TC (12%) GT 6400 22 99.7 AG (86%); GC (14%) TA 6100 0 100.0 TC 6745 13 99.8 TC (50%); AA (25%); GG (25%) TG 5100 3 99.9 AA (100%) TT 6375 6 99.9 AC (50%); CA (50%) ¹Fidelity is calculated as the fraction of correct ligations divided by the total fraction of ligations for a given overhang. ²Top 3 mismatch overhangs are given for each overhang. All overhangs are written in the 5′-to-3′ direction. The numbers in parenthesis give the percentage for the given mismatch ligation relative to the total number of mismatch ligations for the overhang.

TABLE 6 Ligation fidelity for 5-base overhangs (16 hours at 25° C.). This can achieve potentially joining of 512 Fragment in one pot. HgaI Type IIS enzyme is an example of a restriction endonuclease that generates a 5-base overhang. Correct, Mismatch, Fidelity, Overhang ×10⁻⁵ ×10⁻⁵ %¹ Mismatch Overhangs² AAAAA 24 38 38.5 ATTTT (38%); CTTTT (25%); TTTTC (12%) AAAAC 9 99 8.7 GTATT (19%); GTTTC (14%); GTTTA (10%) AAAAG 38 113 25.0 CTATT (17%); CTTTC (17%); CATTT (12%) AAAAT 33 80 29.2 ATTTA (24%); AATTT (24%); ATTTC (18%) AAACA 9 43 18.2 AGTTT (33%); TGTTG (11%); TGTTC (11%) AAACC 9 99 8.7 GGTCT (19%); GGTTA (14%); TGTTT (10%) AAACG 0 156 0.0 CGCTT (15%); CGTTA (12%); CGTAT (12%); CGATT (9%) AAACT 14 113 11.1 AGTTC (21%); AGTTA (17%); AGGTT (12%) AAAGA 24 71 25.0 TCTTC (27%); ACTTT (20%); TCATT (20%) AAAGC 0 109 0.0 GTTTT (13%); GCTTA (13%); ACTTC (9%); ACTTT (9%) AAAGG 43 118 26.5 ACTTT (12%); CCTTA (12%); TCTTT (12%) AAAGT 14 109 11.5 GCTTT (17%); ACATT (17%); ACTTA (13%) AAATA 57 38 60.0 TATTC (25%); AATTT (25%); TATTA (12%) AAATC 14 85 14.3 GATTA (28%); AATTT (17%); GATTG (11%) AAATG 24 85 21.7 CATTA (17%); CATAT (17%); CATTC (11%) AAATT 28 99 22.2 AATCT (14%); TATTT (14%); AATTC (10%) AACAA 5 0 100.0 AACAC 9 52 15.4 GTGCG (9%); GTGCT (9%); GGGTT (9%) AACAG 19 142 11.8 CAGTT (17%); CTGCT (13%); CTATT (10%) AACAT 19 61 23.5 ATGTG (15%); ATGTA (15%); ATCTT (8%) AACCA 14 66 17.6 TGGTC (14%); GGGTT (14%); TTGTT (14%) AACCC 5 85 5.3 CGGTT (17%); GGGTA (17%); GGTTT (17%); GGGGC (11%) AACCG 0 165 0.0 CAGTT (11%); CGGCT (9%); CGGTC (9%); CGGTG (9%) AACCT 14 66 17.6 AGGTA (29%); AAGTT (14%); AGGAT (14%) AACGA 38 109 25.8 ACGTT (26%); TCGTC (17%); TTGTT (9%) AACGC 9 85 10.0 GCGAT (17%); ACGTT (17%); GCGCT (11%) AACGG 0 175 0.0 CCGCT (14%); CCGTA (11%); CCGAT (11%); CCGTG (8%) AACGT 28 123 18.8 ACGAT (23%); ACGTA (15%); CCGTT (15%) AACTA 24 76 23.8 AAGTT (25%); TAGGT (12%); CAGTT (12%) AACTC 9 80 10.5 GAGTG (18%); TAGTT (12%); GAGGT (12%) AACTG 14 118 10.7 CAGTA (16%); CAATT (16%); CAGTG (12%) AACTT 33 52 38.9 AAGCT (27%); AAGAT (27%); AAGTA (18%) AAGAA 43 76 36.0 ATCTT (19%); TTCAT (12%); TTCTA (12%) AAGAC 9 90 9.5 ATCTT (16%); GCCTT (11%); GTCCT (11%) AAGAG 33 90 26.9 CTTTT (21%); CTCTA (11%); CTCAT (11%) AAGAT 9 80 10.5 AACTT (18%); ATCTA (12%); ATCGT (12%) AAGCA 24 85 21.7 AGCTT (17%); TGCTG (17%); TGCGT (11%) AAGCC 9 113 7.7 GTCTT (12%); GGCCT (12%); GGCTG (12%); GGCGC (8%) AAGCG 5 94 4.8 CGCTC (20%); CTCTT (15%); CGCTA (10%); CGCTG (10%) AAGCT 5 99 4.5 AGCTG (24%); AACTT (14%); AGCTA (10%); AGCCT (10%) AAGGA 43 123 25.7 TCCTC (19%); ACCTT (15%); TCTTT (12%) AAGGC 14 156 8.3 GCCAT (18%); GCCTA (12%); ACCTT (9%) AAGGG 24 94 20.0 CCCTA (20%); CCTTT (15%); CCATT (15%) AAGGT 33 66 33.3 ACTTT (14%); ACCAT (14%); ACCTG (7%) AAGTA 28 104 21.4 TACTC (23%); CACTT (14%); TTCTT (14%) AAGTC 5 113 4.0 GACTA (12%); GCCTT (12%); CACTT (12%); GACGG (8%) AAGTG 14 66 17.6 CAATT (21%); CATTT (14%); CACAG (7%) AAGTT 33 85 28.0 AACTA (22%); CACTT (17%); AACTG (11%) AATAA 43 57 42.9 CTATT (25%); GTATT (17%); TTATG (8%) AATAC 14 43 25.0 GAATT (33%); CTATT (11%); GTAAT (11%) AATAG 19 113 14.3 CTATC (17%); CTAAT (12%); CTAGT (12%) AATAT 33 61 35.0 ATAAT (23%); AAATT (15%); ATGTT (15%) AATCA 14 61 18.8 AGATT (31%); TGAAT (23%); TGATC (15%) AATCC 19 109 14.8 GGAAT (22%); GGATA (22%); GGATC (9%) AATCG 5 156 2.9 CGATC (15%); CGATA (12%); CGAAT (12%); CAATT (9%) AATCT 9 80 10.5 TGATT (24%); AAATT (18%); AGAAT (18%) AATGA 33 128 20.6 CCATT (15%); TCAAT (15%); TCATA (11%) AATGC 5 71 6.3 GCATC (20%); GCAAT (13%); GCATA (13%); GCATG (13%) AATGG 14 90 13.6 CCATC (16%); CCAAT (16%); CAATT (11%) AATGT 9 94 9.1 ACGTT (20%); AGATT (10%); CCATT (10%) AATTA 47 61 43.5 CAATT (31%); AAATT (15%); TAATC (8%) AATTC 28 90 24.0 GAATC (21%); GAAAT (11%); AAATT (11%) AATTG 14 90 13.6 CAATG (21%); CAAAT (16%); TAATT (11%) AATTT 28 99 22.2 AAAAT (19%); AAATC (14%); AATTT (10%) ACAAA 19 43 30.8 TTTGA (44%); TCTGT (11%); ATTGT (11%) ACAAC 0 57 0.0 ATTGT (17%); GCTGT (17%); GTTGC (17%); GTTGA (17%) ACAAG 19 109 14.8 CTAGT (13%); CTCGT (13%); CTTGC (13%) ACAAT 14 38 27.3 ATTGA (38%); TTTGT (12%); ATTCT (12%) ACACA 14 76 15.8 TGTGA (31%); TGTGG (25%); AGTGT (12%) ACACC 5 99 4.5 GGTGG (14%); GGTGC (14%); GTTGT (10%); GATGT (10%) ACACG 24 165 12.5 CTTGT (11%); TGTGG (9%); CGAGT (9%) ACACT 5 99 4.5 AGCGT (14%); AGTGA (14%); AGTTT (10%); AGGGT (10%) ACAGA 19 132 12.5 TCTGC (32%); TCTGA (14%); TCTGG (7%) ACAGC 14 90 13.6 GCTGC (21%); GCTAT (16%); ACTGT (11%) ACAGG 5 137 3.3 CCTAT (14%); CCTGC (14%); TCTGT (10%); CCAGT (7%) ACAGT 14 113 11.1 ACTGG (21%); ACTGC (12%); GCTGT (8%) ACATA 24 66 26.3 CATGT (14%); TGTGT (14%); TATGA (14%) ACATC 5 85 5.3 GATGA (22%); GATAT (11%); GAGGT (11%); TATGT (11%) ACATG 14 161 8.1 CATGG (18%); CATGA (15%); CAAGT (12%); CATGC (12%) ACATT 9 80 10.5 AAAGT (24%); AATGA (18%); ACTGT (12%) ACCAA 14 38 27.3 TTGGA (38%); TAGGT (25%); TTGGC (12%) ACCAC 5 52 8.3 GTGGC (18%); GTGGA (18%); GTGAT (18%); GTGGG (9%) ACCAG 14 113 11.1 CTGCT (12%); CTAGT (12%); CTGGC (12%); CTGAT (12%) ACCAT 9 99 8.7 ATGGC (14%); ATGTT (14%); AAGGT (10%) ACCCA 14 43 25.0 AGGGT (22%); TGGAT (11%); GGGGC (11%) ACCCC 0 104 0.0 GGGGA (18%); GGAGT (14%); GGGTT (9%); CGGGT (9%) ACCCG 9 142 6.3 CGGGC (20%); CGGGA (13%); CAGGT (10%); CGGTG (10%) ACCCT 9 94 9.1 AGGGA (25%); AGGGC (15%); TGGGT (15%) ACCGA 14 123 10.3 TCGGC (12%); GCGGC (12%); TAGGT (12%) ACCGC 14 85 14.3 GCGAT (22%); TCGGT (11%); GCAGT (11%) ACCGG 19 161 10.5 CCGGA (21%); CCGAT (18%); CCGGC (9%) ACCGT 5 52 8.3 ACGAT (18%); ACAGT (18%); ACGGA (18%); CCGGT (9%) ACCTA 5 43 10.0 TAGGC (22%); AAGGT (11%); TAGTT (11%); TCGGT (11%) ACCTC 14 61 18.8 GAGGA (38%); AAGGT (8%); ATGGT (8%) ACCTG 28 99 22.2 CAGGA (24%); CAGGG (14%); CCGGT (10%) ACCTT 33 66 33.3 AAGGA (29%); AAGGC (21%); GAGGT (14%) ACGAA 19 113 14.3 TTCGA (29%); TTCGC (21%); TTCAT (12%) ACGAC 9 118 7.4 GACGT (12%); GCCGG (8%); GTCGG (8%) ACGAG 9 118 7.4 CTCGG (16%); CTCGC (12%); CACGT (12%); TTCGT (12%) ACGAT 14 142 9.1 AACGT (20%); ATCGA (17%); ATCGC (10%) ACGCA 5 61 7.1 TGCGG (15%); TGCGA (15%); AGTGT (8%); TGCTT (8%) ACGCC 0 113 0.0 GACGT (8%); GGCGG (8%); GGCCG (4%); AGCGT (4%) ACGCG 5 104 4.3 AGCGT (14%); TGCGG (9%); CGCAT (9%); CGCCT (9%) ACGCT 5 99 4.5 AGAGT (10%); AGCAC (10%); AGCGA (10%); AGCCT (10%) ACGGA 0 156 0.0 TCCGC (27%); TCCGA (12%); TCTGT (9%); ACCGT (6%) ACGGC 14 137 9.4 GCCGA (21%); GCCGC (10%); GCCGG (7%) ACGGG 5 90 5.0 CCCGG (11%); CCCAT (11%); CCCAG (11%); TCCGT (11%) ACGGT 5 104 4.3 GCCGT (9%); GCCGG (9%); ACCAT (9%); ACGGT (9%) ACGTA 14 76 15.8 AACGT (25%); TACGA (12%); TATGT (12%) ACGTC 0 104 0.0 GACGA (9%); GCCGT (9%); GACAT (9%); TACGT (9%) ACGTG 5 94 4.8 CACGA (15%); GACGT (15%); CACAT (10%); CAGGT (10%) ACGTT 28 118 19.4 AACGA (24%); AATGT (16%); AACGC (12%) ACTAA 19 80 19.0 TCAGT (18%); GTAGT (18%); TTAGC (12%) ACTAC 0 57 0.0 GTAGA (25%); GAAGT (17%); ATAGT (17%); GTAGC (8%) ACTAG 28 113 20.0 CTAGA (25%); CTAAT (12%); CAAGT (8%) ACTAT 9 80 10.5 ATAGA (24%); ATGGG (12%); ATGGT (6%) ACTCA 19 52 26.7 AGAGT (27%); TGAAT (18%); CTAGT (9%) ACTCC 9 104 8.3 GAAGT (14%); AGAGT (9%); GTTGT (5%) ACTCG 24 113 17.2 CGAGA (29%); CGAGC (21%); CGATT (12%) ACTCT 9 66 12.5 AGAGC (29%); AGTGT (14%); CGAGT (14%) ACTGA 33 71 31.8 CCAGT (13%); ACAGT (13%); TCAGA (13%) ACTGC 5 85 5.3 GCAGA (22%); ACAGT (17%); GCGGT (17%); GCAGG (11%) ACTGG 5 132 3.4 ACAGT (18%); CAAGT (14%); CTAGT (11%); CCAGA (11%) ACTGT 14 76 15.8 ACAGC (12%); AGAGT (12%); AAAGT (12%) ACTTA 38 104 26.7 TAAGA (18%); TAAGG (18%); GAAGT (14%) ACTTC 5 99 4.5 GAAGA (24%); GAAGC (19%); AAAGC (10%); GAAAT (5%) ACTTG 19 94 16.7 CAAGA (15%); CAAGG (15%); CAATT (15%) ACTTT 14 71 16.7 AAAGA (20%); AAAGG (20%); AAGGT (13%) AGAAA 19 85 18.2 CTTCT (17%); TTACT (17%); TTTCC (11%) AGAAC 14 94 13.0 ATTCT (20%); GTTCA (10%); GTACT (10%) AGAAG 24 142 14.3 CTTCC (23%); CTACT (13%); CTGCT (10%) AGAAT 9 123 7.1 AATCT (12%); ATTCC (12%); CTTCT (12%); GTTCT (12%) AGACA 28 90 24.0 TGTCA (26%); AGTCT (11%); TGGCT (11%) AGACC 14 99 12.5 GGGCT (10%); GGTCG (10%); AGTCT (10%) AGACG 14 137 9.4 CGTCA (14%); CGCCT (10%); CGACT (10%) AGACT 9 85 10.0 AGACT (22%); TGTCT (11%); AGTCG (11%) AGAGA 5 113 4.0 TCTCC (17%); TGTCT (8%); TCCCT (8%); GCTCT (8%) AGAGC 0 109 0.0 ACTCT (17%); GCTCA (13%); GCTTT (13%); GCTCC (13%) AGAGG 14 142 9.1 CCTCA (17%); CCTTT (13%); CCTCG (10%) AGAGT 9 76 11.1 ACTCA (19%); ACGCT (12%); ACTGT (12%) AGATA 24 118 16.7 CATCT (20%); TATCA (16%); TATCC (16%) AGATC 19 156 10.8 GATCC (18%); GATCG (12%); GATAT (9%) AGATG 5 80 5.6 CAACT (29%); CATCC (12%); CTTCT (12%); CATAT (12%) AGATT 9 71 11.8 AATCA (27%); ATTCT (13%); AATGT (13%) AGCAA 9 90 9.5 TTGCA (21%); CTGCT (16%); TCGCT (16%); ATGCT (16%) AGCAC 0 85 0.0 GAGCT (22%); GTGCA (17%); AGGCT (11%); ACGCT (11%) AGCAG 0 109 0.0 CTGCA (17%); CCGCT (13%); CTGAT (13%); CGGCT (9%) AGCAT 0 71 0.0 GTGCT (20%); AAGCT (13%); ATGTT (13%); ATGGG (7%) AGCCA 5 99 4.5 TGGCA (19%); CGGCT (14%); TGGAT (10%); AGGCT (10%) AGCCC 9 85 10.0 CGGCT (22%); GGGCA (17%); GTGCT (11%); GGGCG (11%) AGCCG 9 113 7.7 CGACT (17%); AGGCT (12%); CGGCA (12%); CTGCT (8%) AGCCT 9 123 7.1 AGCCT (23%); AGGCA (15%); ACGCT (8%); AAGCT (8%) AGCGA 9 132 6.7 TCGCC (14%); TCGCA (11%); CCGCT (7%); ACGCT (7%) AGCGC 14 71 16.7 GCACT (13%); GCGCG (13%); ACGCT (13%) AGCGG 0 76 0.0 CCGCC (19%); CAGCT (19%); CCGCG (12%); CTGCT (6%) AGCGT 5 76 5.9 ACGCG (19%); ACACT (19%); ACGTT (12%); GCGCG (6%) AGCTA 5 113 4.0 CAGCT (25%); TAGCA (21%); TAGCG (12%); TAGTT (8%) AGCTC 0 61 0.0 GAGCC (31%); GAGCA (23%); CAGCT (15%); GTGCT (8%) AGCTG 5 104 4.3 AAGCT (23%); CAGTT (14%); CAACT (9%); CAGGA (5%) AGCTT 5 61 7.1 AAGCA (23%); CAGCT (15%); AAGGT (8%); AGGCT (8%) AGGAA 5 94 4.8 TACCT (15%); ATCCT (15%); TTCCA (10%); GACCT (10%) AGGAC 5 128 3.6 GTCTT (11%); GCCCT (11%); GACCT (7%); GTCCC (7%) AGGAG 0 113 0.0 CTCAT (17%); CTCTT (12%); CGCCT (8%); CCCCT (8%) AGGAT 5 66 6.7 ACCCT (14%); ATTCT (14%); AGCCT (14%); AACCT (14%) AGGCA 14 113 11.1 AGCCT (17%); TGCCC (8%); TGCCA (8%) AGGCC 19 113 14.3 GGACT (12%); GGCTT (12%); GGCAT (8%) AGGCG 14 123 10.3 CGCCA (12%); CACCT (12%); TGCCG (8%) AGGCT 9 99 8.7 AGCCG (14%); GGCCG (10%); AGCAC (10%); AGCCA (10%) AGGGA 14 123 10.3 ACCCT (19%); TCCCC (12%); CCCCT (12%) AGGGC 14 94 13.0 ACCCT (15%); GACCT (10%); GCCGT (10%) AGGGG 9 76 11.1 CCCCC (25%); CCCCA (19%); CCTCT (12%) AGGGT 9 94 9.1 ACCCA (10%); CCCCT (10%); GCCCT (10%) AGGTA 19 80 19.0 AACCT (24%); CACCT (18%); GACCT (12%) AGGTC 9 132 6.7 GACAT (14%); GAACT (11%); GACCA (11%) AGGTG 19 80 19.0 CACCC (35%); CACCA (18%); TGCCT (12%) AGGTT 14 66 17.6 AACGT (21%); AAACT (21%); AACCG (21%) AGTAA 0 99 0.0 TTACG (19%); CTACT (14%); TTACC (14%); ATACT (10%) AGTAC 9 57 14.3 GAACT (25%); GCACT (17%); GTAGG (8%) AGTAG 14 94 13.0 CTACA (20%); CCACT (15%); ATACT (15%) AGTAT 14 57 20.0 ATACA (25%); ATACC (17%); ATACG (17%) AGTCA 24 99 19.2 TGACC (19%); TGATT (14%); TGACA (10%) AGTCC 9 99 8.7 GGACA (29%); CGACT (19%); AGACT (10%) AGTCG 19 71 21.1 CGACA (27%); CGATT (13%); AGACT (13%) AGTCT 9 71 11.8 AGACA (13%); AGACC (13%); GGACT (13%) AGTGA 9 94 9.1 CCACT (20%); TCGCT (15%); ACACT (15%); GCACT (10%) AGTGC 19 76 20.0 GCACG (19%); GCACA (12%); GAACT (12%) AGTGG 5 61 7.1 CCGCT (23%); CCACG (15%); TAACT (8%); CAACT (8%) AGTGT 5 71 6.3 ACACA (13%); GCACT (13%); ACTCT (13%); ACACC (7%) AGTTA 28 66 30.0 AAACT (29%); TAACG (21%); TAACC (14%) AGTTC 5 99 4.5 GAACA (24%); AAACT (24%); GATCT (10%); GGACT (10%) AGTTG 9 71 11.8 CAACA (20%); CCACT (20%); CAACG (13%) AGTTT 14 71 16.7 AAACG (20%); AAACA (20%); TAACT (13%) ATAAA 24 52 31.3 TTTAG (18%); TTTGT (9%); TTCAT (9%) ATAAC 14 90 13.6 GTTAA (21%); GTTAG (16%); GTAAT (16%) ATAAG 19 104 15.4 CTCAT (14%); CTTAA (9%); CTTTT (9%) ATAAT 14 76 15.8 ATTAA (31%); AATAT (19%); ATTAC (12%) ATACA 14 76 15.8 AGTAT (19%); TGCAT (12%); CGTAT (12%) ATACC 5 71 6.3 GGAAT (27%); AGTAT (13%); GGTAA (13%); TGTAT (7%) ATACG 38 104 26.7 AGTAT (9%); TGTAT (9%); CGGAT (9%) ATACT 14 90 13.6 AGAAT (16%); AGTAG (16%); TGTAT (11%) ATAGA 9 80 10.5 ACTAT (24%); TATAT (18%); TCAAT (12%) ATAGC 14 90 13.6 GCTAA (37%); GCCAT (16%); GCAAT (11%) ATAGG 14 94 13.0 CCAAT (20%); CCTAC (15%); CCTAG (10%) ATAGT 9 57 14.3 ACTAC (17%); ACAAT (8%); GCTGT (8%) ATATA 52 19 73.3 TATAA (25%); TGAAT (25%); GAAAT (25%) ATATC 14 61 18.8 GATAA (31%); GATAG (23%); GCTAT (15%) ATATG 28 66 30.0 CATAA (21%); CACAT (14%); AATAT (14%) ATATT 33 38 46.7 CATAT (38%); AATAA (12%); AATCT (12%) ATCAA 14 57 20.0 ATGAT (25%); TTGAC (25%); TGGAT (8%) ATCAC 5 33 12.5 GTGGT (29%); GCGAT (14%); GTGCT (14%) ATCAG 14 94 13.0 CGGAT (15%); CTGAG (10%); CTGAC (10%) ATCAT 0 52 0.0 ATGAC (27%); ACGAT (18%); ATGAA (9%); GTGAT (9%) ATCCA 14 61 18.8 TAGAT (23%); GGGAT (23%); TGGTT (15%) ATCCC 5 61 7.1 GGGAA (23%); GGAAT (15%); GGGAC (15%); GGGTT (8%) ATCCG 9 142 6.3 CGGAC (17%); CGGAA (13%); CGAAT (13%); TGGAT (7%) ATCCT 5 71 6.3 TGGAT (20%); AGGAA (20%); CGGAT (13%); GGGAA (7%) ATCGA 9 156 5.7 TCGAC (18%); TCGAA (15%); ACGAT (15%); CCGAT (12%) ATCGC 5 66 6.7 ACGAT (21%); CCGAT (14%); GCAAT (14%); GGGAT (14%) ATCGG 9 71 11.8 CCGAA (13%); CCGAG (13%); ATGAT (7%) ATCGT 14 61 18.8 GCGAT (15%); AAGAT (15%); ACGAC (8%) ATCTA 19 52 26.7 CAGAT (45%); TAGAG (18%); AAGAT (18%) ATCTC 5 52 8.3 GAGAC (27%); GACAT (18%); GAAAT (9%) ATCTG 9 76 11.1 CAGAG (25%); CAGAA (12%); CCGAT (12%) ATCTT 9 57 14.3 AAGAC (25%); AAGAA (25%); ATGAT (8%) ATGAA 43 38 52.9 GTCAT (25%); ATCAT (12%); TTCAG (12%) ATGAC 9 104 8.3 GTCAA (18%); GTCAC (18%); ATCAT (14%) ATGAG 9 76 11.1 CTCAA (19%); CTCTC (12%); CTCCT (12%) ATGAT 0 80 0.0 ATCAA (18%); ATGAT (12%); ACCAT (12%); ATCTT (6%) ATGCA 9 76 11.1 CGCAT (19%); TACAT (19%); TGCAA (19%); TGCAG (12%) ATGCC 0 61 0.0 GGCAA (15%); GGCGT (8%); GGAAT (8%); GTACT (8%) ATGCG 9 90 9.5 GGCAT (11%); CGCAA (11%); CGAAT (11%) ATGCT 0 47 0.0 AGCAA (30%); AGCAG (20%); AACAT (10%); CGCAT (10%) ATGGA 9 94 9.1 TACAT (15%); GCCAT (15%); TCAAT (15%); CCCAT (10%) ATGGC 9 94 9.1 GCTAT (15%); ACCAT (15%); GCCAA (10%) ATGGG 0 71 0.0 CCCAA (20%); ACTAT (13%); CTCAT (7%); TTCAT (7%) ATGGT 9 76 11.1 CCCAT (6%); ACTGT (6%); TGCAG (6%) ATGTA 5 76 5.9 TACAG (12%); CACAT (12%); GACAT (12%); AACAT (12%) ATGTC 9 76 11.1 GACAA (19%); GATAT (12%); CACAT (12%) ATGTG 5 99 4.5 CACAC (14%); CACAA (14%); CTCAT (10%); AACAT (10%) ATGTT 19 80 19.0 ACCAT (18%); AGCAT (12%); AATAT (12%) ATTAA 38 57 40.0 ATAAT (42%); TCAAT (17%); TAAAT (17%) ATTAC 19 38 33.3 ATAAT (25%); GTAAC (12%); GGAAT (12%) ATTAG 38 33 53.3 CCAAT (29%); ATAAT (14%); CAAAT (14%) ATTAT 14 61 18.8 ATAAC (15%); ATTAT (15%); ATATT (8%) ATTCA 38 71 34.8 TGAAA (13%); TAAAT (13%); TGAAG (13%) ATTCC 19 90 17.4 GGAAC (16%); GGAAA (16%); AGAAT (16%) ATTCG 14 85 14.3 CGAAA (17%); CGATT (11%); TGAAT (11%) ATTCT 9 104 8.3 GGAAT (18%); AGAAC (18%); TGAAT (9%); AGATT (9%) ATTGA 28 66 30.0 ACAAT (21%); TCAGT (21%); TCAAC (7%) ATTGC 19 57 25.0 GCAAC (25%); GCAAG (17%); GCAAA (17%) ATTGG 0 85 0.0 CCGAT (11%); CCTAT (11%); CCAAC (11%); CAAAT (11%) ATTGT 14 61 18.8 ACAAC (15%); GGAAT (15%); ACAAA (8%) ATTTA 24 52 31.3 AAAAT (36%); TAAGT (18%); TAAAA (18%) ATTTC 0 80 0.0 AAAAT (18%); GAAAC (12%); TAAAT (12%); CAAAT (12%) ATTTG 9 66 12.5 CAAGT (14%); CCAAT (14%); CTAAT (7%) ATTTT 33 61 35.0 AAAAA (23%); AAAAG (15%); AAGGT (8%) CAAAA 19 47 28.6 CTTTG (20%); ATTTG (10%); TTTGA (10%) CAAAC 9 66 12.5 GTATG (21%); GTTTT (14%); GATTG (14%); GTTCG (14%) CAAAG 9 161 5.6 CTTCG (18%); CTTTA (12%); CATTG (12%); CTATG (9%) CAAAT 9 71 11.8 AATTG (20%); ACTTG (13%); ATTGG (13%) CAACA 19 47 28.6 AGTTG (30%); CGTTG (20%); TGTAG (10%) CAACC 14 85 14.3 GGATG (17%); GGTTA (11%); GGTCG (11%) CAACG 14 113 11.1 CATTG (12%); CGATG (12%); CGTCG (8%) CAACT 9 99 8.7 AGATG (24%); GGTTG (10%); CGTTG (10%) CAAGA 33 151 17.9 TCTAG (16%); CCTTG (12%); TCTTA (12%) CAAGC 14 113 11.1 GCTTA (25%); ACTTG (12%); GCCTG (8%) CAAGG 24 189 11.1 CCTAG (15%); CCTCG (12%); CCATG (12%) CAAGT 19 113 14.3 ACATG (17%); ACTGG (17%); ACTTA (12%) CAATA 14 52 21.4 CATTG (27%); TCTTG (18%); TAGTG (9%) CAATC 5 66 6.7 GCTTG (21%); GAATG (21%); GATCG (14%); GACTG (7%) CAATG 33 80 29.2 AATTG (24%); CAGTG (18%); CACTG (12%) CAATT 14 151 8.6 AACTG (12%); AATTA (12%); ACTTG (9%); AAGTG (9%) CACAA 5 52 8.3 ATGTG (27%); TTGTA (18%); GTGTG (9%) CACAC 5 90 5.0 GTGGG (16%); ATGTG (16%); CACAC (11%); GAGTG (11%) CACAG 19 109 14.8 CCGTG (13%); CTGGG (9%); CGGTG (9%) CACAT 5 76 5.9 ATGTC (12%); ACGTG (12%); CTGTG (12%); ATGTA (12%) CACCA 14 76 15.8 TGGCG (25%); TAGTG (19%); AGGTG (19%); TGGTA (19%) CACCC 9 118 7.4 AGGTG (24%); GAGTG (12%); CGGTG (12%); GGCTG (12%) CACCG 5 118 3.8 CGGTA (20%); CGGCG (16%); CGATG (12%); CGGTC (8%) CACCT 19 99 16.0 AGGTA (14%); AGGCG (14%); AGGTC (10%) CACGA 9 118 7.4 TCGCG (16%); TCGAG (16%); TAGTG (12%); CCGTG (12%) CACGC 9 76 11.1 GCGCG (19%); GCGTA (12%); GTGTG (12%); GCAGG (12%) CACGG 14 109 11.5 CCGAG (17%); CCGCG (13%); CCATG (13%) CACGT 5 43 10.0 ACGAG (33%); ACGCG (22%); ACATG (11%) CACTA 28 66 30.0 CAGTG (21%); TAGTT (7%); TAGCG (7%) CACTC 14 61 18.8 GAATG (23%); GAGTA (15%); GAGGA (8%) CACTG 5 113 4.0 CAGTA (17%); CAGAG (17%); CCGTG (12%); CAGTT (12%) CACTT 14 66 17.6 AAGTC (21%); AAGTA (21%); AAGTT (21%) CAGAA 14 118 10.7 TTCAG (24%); TCCTG (12%); CTCTG (12%) CAGAC 9 85 10.0 GTCTA (22%); GTCTC (17%); GTCAG (11%) CAGAG 24 184 11.4 CTCTA (13%); CACTG (10%); ATCTG (10%) CAGAT 9 76 11.1 ATCTA (31%); TTCTG (19%); AACTG (12%); ATCCG (12%) CAGCA 28 80 26.1 TGCAG (18%); CGCTG (18%); TGCCG (12%) CAGCC 14 109 11.5 GTCTG (13%); TGCTG (9%); GGCTC (9%) CAGCG 14 85 14.3 CGCTC (17%); CGCGG (11%); CACTG (11%) CAGCT 5 142 3.2 AGCTA (20%); AACTG (10%); AGCGG (10%); GACTG (10%) CAGGA 52 156 25.0 ACCTG (15%); GCCTG (12%); TCCTT (9%) CAGGC 0 94 0.0 GCCCG (15%); ACCTG (10%); GCTTG (10%); GCCTT (10%) CAGGG 9 161 5.6 CCCTC (18%); CCCAG (9%); ACCTG (9%); CCCCG (9%) CAGGT 28 90 24.0 ACCCG (16%); ACCGG (11%); ACCAG (11%) CAGTA 14 113 11.1 CACTG (17%); AACTG (17%); TACTA (12%) CAGTC 5 128 3.6 GACTC (22%); CACTG (11%); GAGTG (11%); GACAG (11%) CAGTG 5 118 3.8 AACTG (12%); CACTA (12%); CACGG (12%); CAATG (12%) CAGTT 14 132 9.7 AACAG (18%); AACCG (14%); CACTG (11%) CATAA 33 47 41.2 ATATG (30%); ACATG (10%); TTAGG (10%) CATAC 9 71 11.8 GAATG (13%); GGATG (13%); GCATG (13%) CATAG 14 99 12.5 CTACG (19%); CGATG (14%); CTATC (14%) CATAT 28 109 20.7 ACATG (13%); ATATT (13%); AAATG (13%) CATCA 5 57 7.7 CGATG (25%); TGATA (17%); TCATG (17%); TTATG (8%) CATCC 5 85 5.3 GGAAG (22%); GAATG (17%); GGATC (17%); AGATG (11%) CATCG 5 94 4.8 CGATC (20%); CGATA (20%); CGAAG (15%); CGATT (15%) CATCT 5 80 5.6 AGATA (29%); AGATC (12%); AAATG (12%); AGAGG (6%) CATGA 14 118 10.7 ACATG (20%); TCACG (20%); CCATG (12%) CATGC 5 118 3.8 ACATG (16%); GCAAG (12%); GCACG (12%); GCATA (12%) CATGG 14 109 11.5 ACATG (26%); CCATA (17%); CCAAG (9%) CATGT 14 71 16.7 ACATA (13%); ACAAG (13%); GCATG (13%) CATTA 9 90 9.5 TAAAG (21%); GAATG (16%); AAATG (16%); CATTA (11%) CATTC 9 113 7.7 GAAAG (21%); GAATC (21%); GAATA (21%) CATTG 33 94 25.9 CAAAG (20%); CAACG (15%); CAATA (15%) CATTT 24 85 21.7 AAAAG (17%); AAACG (11%); AAAGG (11%) CCAAA 5 57 7.7 TTAGG (17%); CTTGG (17%); TATGG (17%); TGTGG (8%) CCAAC 9 43 18.2 ATTGG (22%); GCTGG (22%); GTTGT (11%) CCAAG 19 151 11.1 CTTGA (16%); CGTGG (9%); CTGGG (9%) CCAAT 0 99 0.0 ATAGG (19%); AATGG (14%); ATTAG (10%); ATTTG (10%) CCACA 14 66 17.6 CGTGG (21%); TGGGG (21%); TGCGG (14%) CCACC 9 61 13.3 GGTGC (15%); TGTGG (8%); AGTGG (8%) CCACG 0 118 0.0 CGAGG (24%); CTTGG (16%); AGTGG (8%); CGTGA (8%) CCACT 5 90 5.0 AGTGA (21%); AGTTG (16%); AGTAG (16%); AATGG (11%) CCAGA 38 123 23.5 GCTGG (12%); ACTGG (12%); TCTGC (12%) CCAGC 14 109 11.5 GCTAG (17%); ACTGG (13%); GCCGG (13%) CCAGG 19 137 12.1 CCTAG (14%); CCGGG (14%); CCAGG (14%) CCAGT 5 38 11.1 ACAGG (25%); ACTGA (25%); GTTGG (12%); ATTGG (12%) CCATA 14 57 20.0 CATGG (33%); AATGG (17%); TGTGG (8%) CCATC 9 123 7.1 GTTGG (12%); TATGG (12%); AATGG (12%); GAAGG (12%) CCATG 14 99 12.5 CAAGG (24%); CATGA (14%); CACGG (14%) CCATT 14 137 9.4 AATGA (14%); AAGGG (10%); AATAG (10%) CCCAA 9 123 7.1 TCGGG (15%); CTGGG (15%); ATGGG (12%); GTGGG (12%) CCCAC 9 38 20.0 GTTGG (12%); GCGGG (12%); GTGTG (12%) CCCAG 5 113 4.0 CAGGG (12%); CCGGG (12%); CGGGG (12%); CTGAG (8%) CCCAT 0 52 0.0 ACGGG (18%); ATGGA (18%); GTGGG (9%); AGGGG (9%) CCCCA 19 99 16.0 CGGGG (33%); AGGGG (14%); TCGGG (14%) CCCCC 0 99 0.0 AGGGG (19%); CGGGG (14%); GGGGA (14%); GGGGC (10%) CCCCG 0 80 0.0 CGGAG (24%); CAGGG (18%); CGAGG (18%); CGGGC (12%) CCCCT 9 85 10.0 AGGGA (17%); AGGGT (11%); AGGAG (11%) CCCGA 14 57 20.0 GCGGG (17%); CAGGG (17%); CCGGG (17%) CCCGC 5 66 6.7 GGGGG (14%); GCAGG (14%); GTGGG (7%); GCGGA (7%) CCCGG 14 85 14.3 CCCGG (11%); CCGGC (11%); GCGGG (11%) CCCGT 5 38 11.1 AGGGG (12%); ACAGG (12%); AGGGA (12%) CCCTA 0 66 0.0 AAGGG (29%); TCGGG (14%); ATGGG (7%); ACGGG (7%) CCCTC 19 123 13.3 CAGGG (23%); GAAGG (19%); GAGGC (15%) CCCTG 9 24 28.6 AAGGG (40%); TAGGG (20%); CAAGG (20%) CCCTT 24 24 50.0 TAGGG (40%); CAGGG (40%); GAGGG (20%) CCGAA 5 123 3.7 TTCGA (19%); TTCAG (12%); TTAGG (12%); CTCGG (12%) CCGAC 14 99 12.5 GCCGG (14%); GACGG (10%); GTAGG (10%) CCGAG 0 109 0.0 CTCCG (17%); CACGG (17%); CTCAG (13%); ATCGG (9%) CCGAT 9 146 6.1 ACCGG (19%); ATCGA (13%); AACGG (13%) CCGCA 9 76 11.1 TGCAG (25%); TGTGG (12%); TGCGA (12%) CCGCC 9 128 6.9 AGCGG (11%); GGCGA (11%); GACGG (11%); GGCAG (11%) CCGCG 9 161 5.6 CGCCG (15%); CGCGA (12%); CGTGG (9%); CACGG (9%) CCGCT 0 128 0.0 AACGG (19%); AGTGG (11%); AGCAG (11%); AGAGG (7%) CCGGA 19 156 10.8 ACCGG (21%); TCTGG (9%); TACGG (9%) CCGGC 14 161 8.1 GCCGA (12%); ACCGG (9%); GCAGG (9%) CCGGG 14 109 11.5 CCAGG (17%); CCCAG (13%); CCCGA (9%) CCGGT 19 61 23.5 ACCTG (15%); CCCGG (8%); ACCGT (8%) CCGTA 9 80 10.5 AACGG (24%); TAAGG (12%); CACGG (12%) CCGTC 33 113 22.6 GACAG (17%); GACGT (12%); GACGA (12%) CCGTG 14 90 13.6 CACAG (16%); CACTG (16%); CACGA (16%) CCGTT 0 61 0.0 AACGT (31%); ACCGG (15%); AAAGG (15%); GACCG (8%) CCTAA 5 66 6.7 TAAGG (29%); TTAGA (21%); TCAGG (14%); TGAGG (14%) CCTAC 0 61 0.0 ATAGG (23%); CTAGG (15%); GTAGT (15%); TGAGG (8%) CCTAG 28 146 16.2 CAAGG (19%); CCAGG (13%); CTACG (10%) CCTAT 14 71 16.7 ACAGG (27%); ATTGG (13%); TTAGG (13%) CCTCA 24 128 15.6 AGAGG (19%); TGAAG (11%); TGATG (11%) CCTCC 9 128 6.9 GGATG (15%); GCAGG (11%); AGAGG (7%); GGAGA (7%) CCTCG 5 161 2.9 CAAGG (15%); CGACG (12%); AGAGG (9%); CGAGA (9%) CCTCT 14 52 21.4 AGGGG (18%); AGAGA (18%); AAAGG (18%) CCTGA 5 61 7.1 GCAGG (15%); TCATG (15%); TCTGG (8%) CCTGC 5 94 4.8 ACAGG (20%); GCAAG (10%); TCAGG (10%); GCGAG (10%) CCTGG 19 47 28.6 CCTGG (20%); CAAGG (20%); CCAGA (20%) CCTGT 5 24 16.7 AGAGG (40%); AAAGG (20%); TCAGG (20%) CCTTA 28 57 33.3 TCAGG (25%); AAAGG (25%); TGAGG (8%) CCTTC 9 61 13.3 CAAGG (31%); GATGG (15%); AAAGG (15%) CCTTG 24 94 20.0 CAAGA (20%); CCAGG (10%); GAAGG (10%) CCTTT 43 76 36.0 AGAGG (25%); AAGGG (19%); ACAGG (12%) CGAAA 28 99 22.2 TTTTG (14%); ATTCG (14%); TTACG (14%) CGAAC 0 76 0.0 GCTCG (19%); GTACG (19%); GTTCA (12%); GATCG (12%) CGAAG 0 104 0.0 CTTCA (18%); CTACG (14%); CTCCG (14%); CCTCG (14%) CGAAT 14 128 10.0 ATCCG (15%); AATCG (15%); CTTCG (11%) CGACA 9 109 8.0 TGTCA (26%); CGTCG (17%); AGTCG (17%); TGCCG (9%) CGACC 5 113 4.0 GTTCG (21%); CGTCG (12%); GGACG (12%); GGCCG (8%) CGACG 5 161 2.9 CGACG (35%); CCTCG (12%); CGTCA (6%); CGAGG (6%) CGACT 19 109 14.8 AGCCG (17%); AGTCC (17%); AGACG (13%) CGAGA 9 161 5.6 ACTCG (21%); TCTAG (12%); TCGCG (9%); TCACG (9%) CGAGC 9 128 6.9 GCTCA (19%); ACTCG (19%); GCACG (15%); GCTTG (7%) CGAGG 5 123 3.7 CCACG (23%); CCTCA (12%); CCCCG (12%); CCTCC (8%) CGAGT 24 71 25.0 ACACG (20%); ACTCT (13%); AATCG (13%) CGATA 28 109 20.7 AATCG (17%); CATCG (17%); TTTCG (17%) CGATC 0 175 0.0 AATCG (14%); GATCC (11%); GAACG (11%); CATCG (11%) CGATG 5 118 3.8 CAACG (12%); CATAG (12%); CATCA (12%); CACCG (12%) CGATT 5 113 4.0 AAACG (12%); ACTCG (12%); AATAG (12%); CATCG (12%) CGCAA 5 109 4.2 CTGCG (17%); TCGCG (13%); TTGCA (13%); ATGCG (9%) CGCAC 0 43 0.0 GCGCG (22%); CTGCG (22%); GGGTG (11%); GTACG (11%) CGCAG 0 47 0.0 CTACG (20%); CTGCA (20%); CTGCT (10%); GTGCG (10%) CGCAT 9 61 13.3 ATGCA (23%); ACGCG (15%); ATACG (15%) CGCCA 5 118 3.8 CGGCG (28%); AGGCG (12%); TAGCG (8%); TGGCT (8%) CGCCC 5 90 5.0 GGCCG (16%); GAGCG (11%); CGGCG (11%); GGGCA (11%) CGCCG 0 90 0.0 CCGCG (26%); CGGCA (16%); CGGCC (11%); CAGCG (11%) CGCCT 14 85 14.3 AGACG (17%); ACGCG (11%); AGGCA (11%) CGCGA 14 94 13.0 TAGCG (20%); CCGCG (20%); GAGCG (10%) CGCGC 5 90 5.0 TCGCG (11%); GCGCC (11%); GCCCG (11%); GCGCT (11%) CGCGG 9 52 15.4 CAGCG (18%); CCACG (9%); TCGCG (9%) CGCGT 5 28 14.3 ACGAG (17%); ACACG (17%); ATGCG (17%); ACGGG (17%) CGCTA 14 52 21.4 TAGCA (18%); TTGCG (18%); AAGCG (18%) CGCTC 9 90 9.5 AAGCG (21%); CAGCG (16%); GAGCA (16%); GAGAG (16%) CGCTG 14 76 15.8 CAGCA (19%); CAACG (12%); AAGCG (12%) CGCTT 5 61 7.1 AAACG (38%); AATCG (15%); GAGCG (8%); TCGCG (8%) CGGAA 14 137 9.4 TCCCG (21%); ATCCG (14%); TTCCA (10%); TTCTG (10%) CGGAC 5 109 4.2 ATCCG (22%); GGACG (13%); GACCG (9%); TTCCG (9%) CGGAG 19 80 19.0 CCCCG (24%); TTCCG (12%); CTACG (12%) CGGAT 9 90 9.5 ATCAG (16%); AACCG (16%); ATACG (11%); ATCCA (11%) CGGCA 19 137 12.1 TGCGG (10%); GGCCG (10%); TACCG (10%) CGGCC 24 156 13.2 GGCCA (27%); GTGCG (6%); AGCCG (6%) CGGCG 0 128 0.0 CGCCA (26%); CACCG (15%); CGTTG (7%); CGCCC (7%) CGGCT 9 113 7.7 AGCCC (17%); GGCCG (12%); AGCCA (12%); AACCG (12%) CGGGA 5 109 4.2 TACCG (17%); ACCCG (17%); TCCGG (13%); TGCCG (9%) CGGGC 9 165 5.4 ACCCG (17%); GACCG (11%); GCCGG (9%); GCGCG (6%) CGGGG 0 137 0.0 CCCCA (24%); CCCAG (10%); CCCCC (10%); ACCCG (7%) CGGGT 9 128 6.9 TCCCG (11%); GCCCG (11%); GGCCG (7%); ACCCC (7%) CGGTA 14 123 10.3 CACCG (19%); GACCG (12%); TCCCG (12%) CGGTC 14 128 10.0 GACCA (15%); TACCG (11%); GACCC (11%) CGGTG 5 90 5.0 CACCC (16%); ACCCG (16%); AACCG (16%); CACAG (11%) CGGTT 0 94 0.0 AACAG (15%); AACCC (15%); AAACG (10%); ACCCG (10%) CGTAA 19 71 21.1 TAACG (20%); TCACG (13%); TTATG (7%) CGTAC 5 61 7.1 GCACG (23%); GTCCG (23%); GAACG (15%); ATACG (15%) CGTAG 9 33 22.2 CTCAG (14%); CGGCG (14%); CTACT (14%) CGTAT 38 80 32.0 AAACG (24%); ATACA (12%); ACACG (12%) CGTCA 0 109 0.0 AGACG (17%); TGACA (13%); TAACG (13%); TCACG (9%) CGTCC 9 90 9.5 GGACC (21%); TGACG (16%); GGCCG (11%); GGACA (11%) CGTCG 5 104 4.3 CTACG (18%); CGACA (18%); CGACC (14%); CGAAG (9%) CGTCT 14 66 17.6 AGAAG (21%); ACACG (14%); AGAGG (7%) CGTGA 19 61 23.5 ACACG (23%); CCACG (15%); TCAGG (15%) CGTGC 9 94 9.1 GGACG (15%); ACACG (15%); GAACG (10%) CGTGG 0 94 0.0 CCACA (15%); CCAAG (15%); CCGCG (15%); GCACG (10%) CGTGT 24 47 33.3 CCACG (20%); ACATG (10%); ACACA (10%) CGTTA 5 76 5.9 AAACG (25%); TCACG (12%); CAACG (12%); AGACG (6%) CGTTC 9 85 10.0 TAACG (17%); GACCG (11%); GAGCG (11%); CAACG (11%) CGTTG 14 61 18.8 CAACA (15%); CAACT (15%); CGGCG (15%) CGTTT 0 71 0.0 AAAAG (13%); CAACG (13%); GAACG (13%); TAACG (13%) CTAAA 28 52 35.3 TTCAG (18%); TTTAA (18%); TTTCG (18%) CTAAC 5 71 6.3 GATAG (20%); GTAAG (13%); GCAAG (7%); ATTAG (7%) CTAAG 9 61 13.3 CTAAG (15%); CTCAG (15%); CATAG (15%) CTAAT 38 47 44.4 ACTAG (30%); AATAG (30%); ATTTG (10%) CTACA 19 76 20.0 AGTAG (25%); TGCAG (12%); TGTTG (12%) CTACC 9 80 10.5 GGTCG (18%); GGAAG (12%); GGTAA (12%) CTACG 9 137 6.5 CATAG (14%); CGTCG (14%); CCTAG (10%); CGAAG (10%) CTACT 14 94 13.0 AGAAG (20%); TGTAG (20%); AGTAA (15%) CTAGA 24 104 18.5 ACTAG (27%); TCTAA (14%); TCTGG (9%) CTAGC 5 76 5.9 GCGAG (19%); GCAAG (12%); ACTAG (12%); GCCAG (12%) CTAGG 28 90 24.0 CCAAG (16%); CCTCG (11%); CCTAC (11%) CTAGT 28 118 19.4 GCTAG (12%); ACTGG (12%); AATAG (12%) CTATA 28 33 46.2 TATTG (43%); CATAG (14%); TAGAG (14%) CTATC 14 118 10.7 GAAAG (20%); AATAG (16%); GATAA (16%) CTATG 14 76 15.8 CAAAG (19%); CATCG (12%); CTTAG (12%) CTATT 19 90 17.4 AAAAG (21%); AACAG (16%); AATAA (16%) CTCAA 24 85 21.7 CTGAG (17%); ATGAG (17%); TTGAC (11%) CTCAC 5 90 5.0 GCGAG (26%); GAGAG (11%); GTAAG (11%); GTGGG (5%) CTCAG 5 94 4.8 CCGAG (15%); CGGAG (10%); CTAAG (10%); CAGAG (10%) CTCAT 9 94 9.1 AGGAG (20%); ATAAG (15%); TTGAG (15%); AAGAG (10%) CTCCA 5 80 5.6 TGTAG (12%); TGAAG (12%); AGGAG (12%); GGGAG (12%) CTCCC 14 47 23.1 GGGAT (20%); TGGAG (20%); GGGCG (20%) CTCCG 19 80 19.0 CCGAG (24%); CGAAG (18%); CAGAG (18%) CTCCT 0 76 0.0 CGGAG (12%); ACGAG (12%); ATGAG (12%); AGGAA (12%) CTCGA 24 80 22.7 TCAAG (18%); TCCAG (12%); CCGAG (12%) CTCGC 5 99 4.5 GCAAG (14%); GCGAA (14%); ACGAG (14%); GCCAG (14%) CTCGG 0 128 0.0 CAGAG (15%); ACGAG (15%); CCGAA (11%); CCTAG (7%) CTCGT 9 66 12.5 ACAAG (21%); AAGAG (14%); GCGCG (7%) CTCTA 9 71 11.8 CAGAG (33%); AAGAG (13%); TTGAG (13%) CTCTC 9 94 9.1 CAGAG (15%); GAAAG (10%); GATAG (10%); AAGAG (10%) CTCTG 24 80 22.7 CAGAA (18%); TAGAG (12%); CTGAG (6%) CTCTT 33 99 25.0 TAGAG (19%); AAGCG (14%); AGGAG (14%) CTGAA 33 71 31.8 TCCAG (27%); TTCTG (20%); TTTAG (13%) CTGAC 5 99 4.5 GACAG (24%); GTCAA (14%); ATCAG (10%); GTTGG (10%) CTGAG 5 90 5.0 CTCAA (16%); CTGAG (11%); ATCAG (11%); TTCAG (11%) CTGAT 14 90 13.6 TTCAG (16%); AGCAG (16%); ACCAG (16%) CTGCA 9 113 7.7 AGCAG (17%); TACAG (17%); TTCAG (8%); GGCAG (8%) CTGCC 0 104 0.0 GGCCG (18%); GGCAA (18%); GGCAC (14%); TGCAG (9%) CTGCG 0 99 0.0 CGCAA (19%); CACAG (10%); CGCAC (10%); CGCTG (10%) CTGCT 0 123 0.0 AACAG (15%); AGCAA (12%); AGAAG (12%); ACCAG (12%) CTGGA 33 99 25.0 TCCTG (10%); TCCGG (10%); TACAG (10%) CTGGC 5 113 4.0 GACAG (21%); GCTAG (12%); ACCAG (12%); GGCAG (8%) CTGGG 5 104 4.3 CCCAA (18%); CCAAG (14%); CACAG (9%); CCCGG (9%) CTGGT 14 71 16.7 ATCAG (13%); ACCTG (13%); ACTAG (13%) CTGTA 14 52 21.4 CACAG (18%); AACAG (18%); TCCAG (18%) CTGTC 19 90 17.4 GACGG (11%); GACTG (11%); GGCAG (11%) CTGTG 19 71 21.1 AACAG (13%); CACAT (13%); CCTAG (7%) CTGTT 19 104 15.4 AACCG (14%); GACAG (14%); AACTG (9%) CTTAA 24 66 26.3 ATAAG (14%); TCAAG (14%); TTAAT (7%) CTTAC 9 71 11.8 GAAAG (33%); GTTAG (13%); ATAAG (13%) CTTAG 9 66 12.5 CAAAG (21%); CTATG (14%); ATAAG (14%) CTTAT 19 66 22.2 AAAAG (21%); CTAAG (14%); ATGAG (14%) CTTCA 28 80 26.1 CGAAG (24%); AGAAG (18%); TGAAA (12%) CTTCC 9 113 7.7 AGAAG (29%); GGAAA (25%); GAAAG (12%); GGAAC (8%) CTTCG 0 118 0.0 CAAAG (24%); AGAAG (12%); CGAAT (12%); CCAAG (8%) CTTCT 24 80 22.7 AGAAA (18%); AGAAT (18%); AGACG (12%) CTTGA 9 99 8.7 CCAAG (24%); TCGAG (14%); ACAAG (14%); TCAGG (10%) CTTGC 19 71 21.1 ACAAG (20%); GCTAG (13%); GCAAT (13%) CTTGG 19 80 19.0 CCACG (24%); CCCAG (12%); ACAAG (12%) CTTGT 19 76 20.0 ACACG (25%); CCAAG (19%); ACATG (12%) CTTTA 33 66 33.3 CAAAG (29%); GAAAG (29%); AAAAG (14%) CTTTC 19 99 16.0 AAAAG (19%); GAACG (14%); GAAAA (10%) CTTTG 9 94 9.1 CCAAG (15%); CACAG (10%); CAAAA (10%); CAGAG (10%) CTTTT 38 80 32.0 AAGAG (24%); ATAAG (12%); AAAAA (12%) GAAAA 28 71 28.6 TCTTC (20%); TTTTA (13%); TATTC (13%) GAAAC 19 170 10.0 GTTAC (14%); GTCTC (11%); GTGTC (11%) GAAAG 19 142 11.8 CATTC (17%); CTTAC (17%); CTATC (17%) GAAAT 0 61 0.0 AATTC (15%); GTTTC (15%); GTTTT (8%); ACTTC (8%) GAACA 28 137 17.1 AGTTC (17%); TGCTC (17%); TGATC (10%) GAACC 9 94 9.1 TGTTC (10%); GGATC (10%); GGTCC (10%) GAACG 9 128 6.9 CGATC (15%); CTTTC (11%); CGTGC (7%) GAACT 5 123 3.7 AGGTC (12%); AGATC (12%); AGTAC (12%); GGTTA (8%) GAAGA 19 109 14.8 ACTTC (22%); TCATC (13%); TCTTT (13%) GAAGC 9 142 6.3 GCTAC (17%); GCTCC (13%); ACTTC (13%); GCCTC (10%) GAAGG 9 99 8.7 CCCTC (24%); CCATC (14%); CCTCC (10%); CCTTG (10%) GAAGT 5 90 5.0 ACTTA (16%); ACTCC (16%); ACGTC (11%); TCTTC (11%) GAATA 28 94 23.1 CATTC (25%); TAATC (15%); TTTTC (10%) GAATC 14 161 8.1 CATTC (15%); GTTTC (15%); GGTTC (12%); AATTC (12%) GAATG 9 104 8.3 CATCC (14%); CAATC (14%); CATTA (14%); CACTC (14%) GAATT 28 61 31.6 AATAC (23%); ATTTC (15%); AAGTC (15%) GACAA 24 118 16.7 TAGTC (28%); TCGTC (12%); ATGTC (12%) GACAC 14 94 13.0 GTGAC (15%); ATGTC (10%); GTATC (10%) GACAG 19 170 10.0 CTGGC (14%); CTGAC (14%); CCGTC (11%) GACAT 9 94 9.1 AGGTC (20%); CTGTC (10%); ACGTC (10%) GACCA 9 128 6.9 CGGTC (15%); AGGTC (11%); TGGAC (11%); GGGTC (11%) GACCC 5 61 7.1 CGGTC (23%); GAGTC (23%); AGGTC (15%); GGGGC (8%) GACCG 14 132 9.7 CGGGC (14%); CGATC (11%); CGGTA (11%) GACCT 9 109 8.0 TGGTC (9%); AGATC (9%); AGGGC (9%) GACGA 14 123 10.3 TCGAC (15%); TCATC (12%); CCGTC (12%) GACGC 0 24 0.0 GTGTC (20%); AGGTC (20%); CCGTC (20%); AAGTC (20%) GACGG 33 113 22.6 CCGCC (12%); CCGCT (8%); ACGGC (8%) GACGT 0 94 0.0 ACGAC (15%); ACGTG (15%); CCGTC (15%); ACGCC (10%) GACTA 28 76 27.3 TTGTC (19%); AAGTC (19%); TGGTC (12%) GACTC 14 128 10.0 CAGTC (22%); GAGCC (19%); GAGAC (11%) GACTG 5 113 4.0 CAGCT (12%); CAGTA (8%); CTGTT (8%); CCGTC (8%) GACTT 5 76 5.9 AAGAC (12%); AAGTA (12%); GAGTC (12%); TTGTC (6%) GAGAA 9 170 5.3 TTCAC (14%); TTCGC (11%); TTCTT (11%); TACTC (8%) GAGAC 14 109 11.5 GGCTC (13%); ATCTC (13%); GTCTT (13%) GAGAG 9 104 8.3 CGCTC (14%); CCCTC (9%); CTGTC (9%) GAGAT 5 33 12.5 ATCTT (14%); ATCGG (14%); AGCTC (14%) GAGCA 5 80 5.6 CGCTC (18%); AGCTC (18%); TGCCC (12%); TACTC (12%) GAGCC 0 137 0.0 GACTC (17%); AGCTC (14%); GGCTA (10%); GTCTC (7%) GAGCG 9 90 9.5 CGTTC (11%); CGGTC (11%); CGCGA (11%) GAGCT 0 80 0.0 AGCAC (24%); AGATC (18%); AGTTC (12%); AGCTA (6%) GAGGA 5 113 4.0 ACCTC (21%); TCCAC (17%); TCTTC (8%); TTCTC (8%) GAGGC 5 113 4.0 CCCTC (17%); GCCTA (12%); GTCTC (12%); GCATC (8%) GAGGG 19 57 25.0 CCCGA (17%); CCCAA (8%); CCTCC (8%) GAGGT 14 66 17.6 AACTC (14%); ACATC (14%); ACCTT (14%) GAGTA 14 71 16.7 TCCTC (20%); TACAC (20%); CACTC (13%) GAGTC 14 57 20.0 GACCC (25%); GCCTC (25%); GACTT (17%) GAGTG 14 113 11.1 AACTC (12%); CACCC (12%); CAGTC (12%) GAGTT 9 43 18.2 AACTA (22%); GACTC (22%); ATCTC (11%) GATAA 38 109 25.8 CTATC (17%); ATATC (17%); TAATC (9%) GATAC 14 109 11.5 GCATC (13%); GAATC (13%); GTATA (9%) GATAG 14 85 14.3 CTAAC (17%); ATATC (17%); CTCTC (11%) GATAT 14 57 20.0 AGATC (25%); ACATC (17%); ATGTC (17%) GATCA 14 123 10.3 CGATC (12%); TGATA (12%); AGATC (12%) GATCC 24 123 16.1 AGATC (23%); CGATC (15%); GGCTC (8%) GATCG 0 99 0.0 AGATC (19%); CGACC (10%); CGAAC (10%); CGAGC (10%) GATCT 19 76 20.0 AGTTC (12%); AGAAC (12%); AGGTC (6%) GATGA 14 90 13.6 ACATC (21%); TCATA (11%); TCATT (11%) GATGC 5 85 5.3 GCATA (22%); GCAAC (17%); CCATC (11%); GAATC (11%) GATGG 9 80 10.5 CGATC (18%); CCTTC (12%); CCATT (12%) GATGT 5 71 6.3 ACATA (13%); CCATC (13%); ACACC (13%); ACAAC (7%) GATTA 14 71 16.7 AAATC (33%); TAAGC (27%); TAACC (13%) GATTC 14 57 20.0 GAAGC (25%); TAATC (8%); GAAAC (8%) GATTG 5 52 8.3 AAATC (18%); CAAAC (18%); TAATC (9%); CAATT (9%) GATTT 14 80 15.0 AAAAC (12%); AAACC (12%); GAATC (12%) GCAAA 14 52 21.4 ATTGC (18%); TTTGA (18%); TTCGC (18%) GCAAC 0 109 0.0 GTAGC (17%); ATTGC (13%); GATGC (13%); GTCGC (9%) GCAAG 19 85 18.2 CATGC (17%); CTCGC (17%); ATTGC (11%) GCAAT 19 85 18.2 ATAGC (11%); CTTGC (11%); ATCGC (11%) GCACA 9 94 9.1 TGAGC (10%); TGTAC (10%); TGTGA (10%); TATGC (10%) GCACC 5 90 5.0 GGCGC (11%); GGAGC (11%); GGTGA (11%); TGTGC (11%) GCACG 9 146 6.1 CGAGC (13%); AGTGC (10%); CATGC (10%); CGTAC (10%) GCACT 19 76 20.0 AGTGT (12%); AGTGA (12%); AGTAC (12%) GCAGA 33 128 20.6 ACTGC (15%); TCTGG (15%); TCGGC (7%) GCAGC 0 104 0.0 GCTAC (9%); GCTGA (9%); GCTTC (9%); ACTGC (5%) GCAGG 5 146 3.1 CCTCC (10%); CCGGC (10%); ACTGC (6%); CCCGC (6%) GCAGT 5 71 6.3 ACCGC (13%); ACTGT (13%); ACTTC (7%) GCATA 28 94 23.1 GATGC (20%); TATGA (20%); CATGC (15%) GCATC 5 99 4.5 GATAC (14%); AATGC (14%); GATCC (10%); TATGC (10%) GCATG 5 80 5.6 CATGT (12%); CATAC (12%); CCTGC (12%); AATGC (12%) GCATT 5 71 6.3 AATGA (20%); CATGC (13%); TATGC (13%); ACTGC (7%) GCCAA 5 109 4.2 TCGGC (22%); TTGGA (13%); TTGAC (13%); TGGGC (9%) GCCAC 5 94 4.8 GTAGC (15%); ATGGC (10%); GAGGC (10%); GGGGC (10%) GCCAG 5 146 3.1 CTCGC (10%); ATGGC (6%); CTGGG (6%); CTAGC (6%) GCCAT 9 128 6.9 AAGGC (22%); ATAGC (11%); ATGGA (11%); TTGGC (11%) GCCCA 14 76 15.8 TCGGC (12%); TGGTC (12%); TAGGC (12%) GCCCC 5 90 5.0 GGGAC (26%); GGGAA (11%); GCGGC (11%); GAGGC (11%) GCCCG 9 142 6.3 CGGGT (10%); CAGGC (10%); CGGAC (7%) GCCCT 14 109 11.5 AGGAC (13%); AGGTC (9%); AGGGA (9%) GCCGA 14 137 9.4 ACGGC (21%); CCGGC (14%); TCGTC (10%) GCCGC 9 118 7.4 TCGGC (12%); GCGAC (12%); ACGGC (12%); GCTGC (12%) GCCGG 14 142 9.1 CGGGC (10%); CCAGC (10%); CCGAC (10%) GCCGT 14 76 15.8 ACGGA (12%); ACGTC (12%); AGGGC (12%) GCCTA 5 104 4.3 AAGGC (18%); TCGGC (14%); GAGGC (14%); TAGGT (14%) GCCTC 5 104 4.3 GAAGC (14%); GAGTC (14%); GTGGA (9%); AAGGC (9%) GCCTG 0 90 0.0 CAGGA (21%); CCGGC (11%); CAGGG (11%); CAAGC (11%) GCCTT 14 80 15.0 AAGTC (18%); AAGAC (12%); AAAGC (12%) GCGAA 5 66 6.7 CTCGC (21%); TTCGA (21%); TCCGC (14%); GTTGC (7%) GCGAC 5 66 6.7 GCCGC (21%); GTCGA (7%); GTTGT (7%); GTTGC (7%) GCGAG 5 94 4.8 CTCAC (25%); CTAGC (15%); CCTGC (10%); CTCAT (5%) GCGAT 5 90 5.0 ACCGC (21%); AACGC (16%); ATCGA (16%); ATCGT (11%) GCGCA 5 76 5.9 TGCGG (12%); GGCGC (12%); AGCGT (6%); CGGGC (6%) GCGCC 5 151 3.0 GGCGG (16%); GGAGC (9%); GGCGA (9%); GGCGT (9%) GCGCG 5 123 3.7 CACGC (12%); CGGGC (8%); CGCAC (8%); CGCTC (8%) GCGCT 14 90 13.6 AACGC (11%); CGCGC (11%); AGCGA (11%) GCGGA 14 85 14.3 TCCAC (17%); TCCCC (6%); CCCGC (6%) GCGGC 9 123 7.1 ACCGA (12%); GGCGC (8%); GCCGG (8%); GCCCC (8%) GCGGG 5 109 4.2 TCCGC (13%); CCCGG (9%); CCCGA (9%); CCGGC (9%) GCGGT 14 94 13.0 ACTGC (15%); ACCCC (10%); TCCGC (10%) GCGTA 9 33 22.2 CACGC (29%); TACGA (14%); TACTC (14%) GCGTC 0 43 0.0 GACGA (22%); GACGG (11%); GGCTC (11%); GCCGT (11%) GCGTG 9 57 14.3 CATGA (17%); CGGGC (8%); CACAC (8%) GCGTT 9 66 12.5 AAGGC (14%); AACTC (7%); TAGGC (7%) GCTAA 9 85 10.0 ATAGC (39%); TTAGT (11%); TCAGC (11%) GCTAC 5 99 4.5 GAAGC (24%); GTAGA (10%); GCAGC (10%); GTCGC (10%) GCTAG 5 123 3.7 CCAGC (15%); CTAGT (12%); CTGGC (12%); TTAGC (8%) GCTAT 14 118 10.7 ACAGC (12%); ATGGC (12%); TTAGC (8%) GCTCA 14 94 13.0 CGAGC (25%); TCAGC (15%); AGAGC (15%) GCTCC 5 90 5.0 GAAGC (21%); GGAAC (16%); AGAGC (16%); GGACC (11%) GCTCG 9 90 9.5 CGATC (16%); CGAAC (16%); CCAGC (11%) GCTCT 0 33 0.0 AGAGA (29%); GGAGC (14%); TGAGC (14%); AGCGA (14%) GCTGA 0 61 0.0 GCAGC (15%); TGAGC (15%); TCAGA (15%); TCTGC (8%) GCTGC 0 85 0.0 ACAGC (22%); GCCGC (17%); GCGGC (11%); GCTGC (11%) GCTGG 14 85 14.3 CCAGA (17%); CCAAC (11%); CAAGC (11%) GCTGT 14 80 15.0 ACAAC (12%); ACAGT (12%); AGAGC (12%) GCTTA 43 113 27.3 CAAGC (25%); TAAGA (12%); AAAGC (12%) GCTTC 9 47 16.7 GCAGC (20%); TAAGC (20%); CAAGC (20%) GCTTG 14 94 13.0 CAATC (15%); CAAGA (10%); AAAGC (10%) GCTTT 0 94 0.0 TAAGC (20%); AAAGT (20%); AGAGC (15%); CAAGC (10%) GGAAA 43 132 24.3 CTTCC (21%); TTTCT (14%); ATTCC (11%) GGAAC 14 104 12.0 GTTCA (18%); GTCCC (14%); ATTCC (14%); GCTCC (14%) GGAAG 9 94 9.1 CATCC (20%); TTTCC (10%); CTTTC (10%); CTACC (10%) GGAAT 19 128 12.9 AATCC (19%); ATTCT (15%); ATACC (15%) GGACA 38 146 20.5 AGTCC (19%); TGACC (13%); TGTTC (10%) GGACC 5 137 3.3 CGTCC (14%); TGTCC (14%); GCTCC (7%); GGGCC (7%) GGACG 9 123 7.1 CGACC (12%); CGGAC (12%); CGTGC (12%); CGGCC (8%) GGACT 9 113 7.7 AGGCC (12%); AGTCT (8%); AGTTC (8%); TGTCC (8%) GGAGA 9 85 10.0 TTTCC (17%); TCACC (17%); CCTCC (11%) GGAGC 5 128 3.6 GCGCC (11%); GCTCA (7%); GCTAC (7%); GCACC (7%) GGAGG 9 90 9.5 CCGAC (11%); CCCCA (5%); CATAC (5%) GGAGT 9 85 10.0 ACCCC (17%); CCTCC (11%); GATCC (11%) GGATA 14 90 13.6 AATCC (26%); TATCA (11%); TAGCC (11%) GGATC 24 80 22.7 CATCC (18%); GCTCC (12%); GAACC (12%) GGATG 5 85 5.3 CCTCC (22%); CAACC (17%); CATAC (11%); AATCC (11%) GGATT 19 80 19.0 AATTC (12%); GATCC (12%); ATTCC (12%) GGCAA 5 151 3.0 TCGCC (19%); CTGCC (12%); TTACC (12%); TTGCA (9%) GGCAC 5 71 6.3 CTGCC (20%); GTCCC (7%); GTGCT (7%); GGCCC (7%) GGCAG 0 118 0.0 CCGCC (12%); CTGCA (8%); CTGGC (8%); CTGTC (8%) GGCAT 0 85 0.0 ATGCG (11%); TTGCC (11%); AGGCC (11%); GTGCC (11%) GGCCA 5 137 3.3 CGGCC (31%); TGGAC (7%); TGTCC (7%); GGGCC (7%) GGCCC 5 118 3.8 GGCCC (16%); GGACC (8%); GGGCT (8%); CGGCC (8%) GGCCG 24 179 11.6 CTGCC (11%); CGGCA (8%); CGGCT (8%) GGCCT 19 99 16.0 AAGCC (14%); AGGCA (10%); AGGAC (10%) GGCGA 14 123 10.3 GCGCC (12%); CCGCC (12%); TCACC (8%) GGCGC 5 113 4.0 GCACC (8%); GCGGC (8%); AAGCC (8%); GCGCA (8%) GGCGG 9 104 8.3 GCGCC (23%); ACGCC (9%); CCGCG (9%); CAGCC (9%) GGCGT 0 85 0.0 GCGCC (17%); ACGTA (6%); TAGCC (6%); AGGCC (6%) GGCTA 14 85 14.3 GAGCC (17%); TAGGC (11%); TTGCC (11%) GGCTC 0 104 0.0 GCGCC (14%); GAGAC (14%); GTGCT (9%); GATCC (9%) GGCTG 14 76 15.8 CACCC (19%); AAGCC (19%); CGGCC (6%) GGCTT 9 71 11.8 AGGCC (20%); AAGCT (13%); AAGAC (7%) GGGAA 24 85 21.7 ATCCC (17%); TCCCC (11%); GTCCC (11%) GGGAC 5 109 4.2 GCCCC (22%); GTCCA (9%); ATCCC (9%); GTGCC (9%) GGGAG 14 61 18.8 CTCCA (15%); CGCCC (15%); CTACA (8%) GGGAT 5 66 6.7 ATCCA (21%); ACCCC (14%); ATCGC (14%); CTCCC (14%) GGGCA 14 146 8.8 TACCC (10%); AGCCC (10%); TCCCC (6%) GGGCC 5 118 3.8 GGACC (8%); GGGCC (8%); GGCCA (8%); AGCCC (8%) GGGCG 5 66 6.7 TGCCC (14%); AGCCC (14%); CTCCC (14%); CGACC (7%) GGGCT 9 104 8.3 AGACC (9%); GGCCA (9%); AGCAC (9%); GGCCC (9%) GGGGA 9 61 13.3 ACCCC (31%); CCCCC (23%); GTCCC (8%) GGGGC 5 109 4.2 TCCCC (9%); GCCAC (9%); AACCC (9%); CCCCC (9%) GGGGG 0 43 0.0 CCCGC (22%); CCTTC (11%); TCCCC (11%); CCTCC (11%) GGGGT 0 38 0.0 ACCCT (12%); GCCCT (12%); ACTCC (12%); GGCCC (12%) GGGTA 5 66 6.7 TGCCC (21%); AACCC (21%); TCCCC (7%); TAGCC (7%) GGGTC 5 99 4.5 GACCA (14%); CACCC (10%); TACCC (10%); AACCC (10%) GGGTG 9 104 8.3 CACCT (9%); CACAC (9%); CCCCC (9%) GGGTT 5 61 7.1 ACCCC (15%); AACCA (15%); GACCT (8%); AGCCT (8%) GGTAA 19 90 17.4 TCACC (16%); ATACC (11%); CTACC (11%) GGTAC 14 52 21.4 GAGCC (18%); GAACC (18%); CGACC (9%) GGTAG 9 38 20.0 CTGCT (12%); CTAGA (12%); CTGCA (12%) GGTAT 5 61 7.1 TTACC (23%); ATACT (15%); ATAAC (8%) GGTCA 5 118 3.8 TGACA (12%); TAACC (12%); AGACC (8%); TGACG (8%) GGTCC 5 109 4.2 CGACC (9%); GGAAC (9%); AGACC (9%); GGCCC (9%) GGTCG 5 80 5.6 CTACC (18%); AGACC (12%); TGGCC (12%); CAACC (12%) GGTCT 14 80 15.0 AAACC (24%); AGACA (12%); GGACC (6%) GGTGA 9 38 20.0 GCACC (25%); TCTCC (25%); TCACA (12%) GGTGC 5 66 6.7 ACACC (21%); CCACC (14%); GCAGC (7%); GGACC (7%) GGTGG 9 90 9.5 ACACC (16%); CCACT (11%); CCACA (5%) GGTGT 5 43 10.0 ACCCC (11%); ACGCA (11%); ACGCT (11%) GGTTA 24 80 22.7 AAACC (18%); TAAAC (12%); GAACT (12%) GGTTC 9 71 11.8 GAATC (27%); GAAAC (20%); GAACA (13%) GGTTG 14 61 18.8 CAACT (15%); CGGCC (8%); CTAAC (8%) GGTTT 9 90 9.5 AACCC (16%); ATTCC (11%); ATACC (5%) GTAAA 38 76 33.3 TTTAT (19%); TTTTC (12%); GTTAC (12%) GTAAC 0 80 0.0 GTGAC (18%); GTAAC (12%); GTTAA (12%); GTTTC (12%) GTAAG 9 90 9.5 CTAAC (11%); CTTTC (11%); CTGAC (11%); CTCAC (11%) GTAAT 19 57 25.0 ATAAC (25%); ATGAC (17%); TTTAC (17%) GTACA 14 33 30.0 TGCAC (29%); AGTAC (14%); CGTAC (14%) GTACC 14 80 15.0 GATAC (6%); GTAAC (6%); GGAAC (6%) GTACG 5 71 6.3 CGAAC (20%); CGTTC (7%); CGACC (7%) GTACT 9 52 15.4 AGAAC (18%); GATAC (9%); AGTAT (9%) GTAGA 14 76 15.8 ACTAC (19%); GCTAC (12%); TCCAC (12%) GTAGC 5 71 6.3 GCAAC (27%); GCCAC (20%); GCTAA (7%); GCTAG (7%) GTAGG 0 71 0.0 CCTAG (13%); CCGAC (13%); CCTCC (7%); ACTAT (7%) GTAGT 0 76 0.0 ACTAA (19%); CCTAC (12%); AATAC (6%); ACTGC (6%) GTATA 24 66 26.3 TGTAC (21%); GATAC (14%); TATAT (14%) GTATC 14 57 20.0 GATAA (17%); GACAC (17%); GATAT (8%) GTATG 9 24 28.6 CAAAC (60%); CATAT (40%) GTATT 14 76 15.8 AAAAC (25%); GAAAC (19%); AATAA (12%) GTCAA 14 142 9.1 ATGAC (13%); TCGAC (13%); CTGAC (10%); TGGAC (10%) GTCAC 0 71 0.0 ATGAC (27%); GTAAC (13%); GGGAC (13%); GTCAC (13%) GTCAG 5 80 5.6 CAGAC (12%); CGGGC (6%); ATGAC (6%); TTGAC (6%) GTCAT 9 43 18.2 ATGAA (22%); ATAAC (22%); TTGGC (11%) GTCCA 9 94 9.1 TGAAC (15%); TAGAC (10%); AGGAC (10%) GTCCC 5 85 5.3 GGAAC (17%); GGGAA (11%); AGGAC (11%); GAGAC (11%) GTCCG 5 66 6.7 CGTAC (21%); CGGGC (14%); CGGCC (14%); CGGAA (14%) GTCCT 5 71 6.3 AAGAC (13%); AGGTC (13%); AGAAC (13%); AGGGG (7%) GTCGA 14 38 27.3 TGGAC (12%); ACGAC (12%); GCGAC (12%) GTCGC 5 66 6.7 GCTAC (14%); GCAAC (14%); ACGAT (14%); GAGAC (14%) GTCGG 14 71 16.7 ACGAC (13%); ACGAT (13%); CCGAT (7%) GTCGT 9 43 18.2 AAGAC (11%); ACAGC (11%); GCTAC (11%) GTCTA 5 85 5.3 CAGAC (22%); TAGAT (17%); TCGAC (11%); AAGAC (6%) GTCTC 14 99 12.5 GAAAC (19%); GAGGC (14%); CAGAC (14%) GTCTG 9 76 11.1 CAGCC (19%); TAGAA (12%); TAGAC (12%); CAGGC (12%) GTCTT 9 80 10.5 AAGCC (18%); AGGAC (18%); GAGAC (18%); AAAAC (12%) GTGAA 24 52 31.3 TCCAC (18%); TGCAC (9%); TTCCC (9%) GTGAC 0 76 0.0 GTAAC (19%); GACAC (19%); GGCTC (6%); ATAAC (6%) GTGAG 5 52 8.3 CCCAA (9%); CACAC (9%); CTAAC (9%); CTACC (9%) GTGAT 5 52 8.3 ACCAC (18%); ATCAG (9%); ATCAT (9%) GTGCA 5 90 5.0 AGCAC (16%); TGCAA (11%); TACAC (11%); TTCAC (5%) GTGCC 5 76 5.9 GGCAT (12%); GACAC (12%); GGGAC (12%); GTGCC (12%) GTGCG 0 66 0.0 CGGCC (14%); CCCTC (7%); CGCCA (7%); TGTAC (7%) GTGCT 0 80 0.0 AGCAT (18%); GGCTC (12%); AGCCC (12%); CGCGC (6%) GTGGA 5 76 5.9 TACAC (19%); TCAAC (12%); ACCAC (12%); GCCTC (12%) GTGGC 5 109 4.2 TCCAC (9%); GCAAC (9%); ACCAC (9%); GCTAT (9%) GTGGG 9 66 12.5 CCCAA (21%); CACAC (21%); CTCAT (7%) GTGGT 5 66 6.7 ACCCC (14%); ATCAC (14%); CACAC (7%) GTGTA 5 28 14.3 GATAC (17%); TACCC (17%); TAGAC (17%); TACAA (17%) GTGTC 14 80 15.0 GAAAC (24%); GACAA (12%); TACAC (12%) GTGTG 5 57 7.7 CACGC (17%); CATAC (8%); CCCGC (8%) GTGTT 9 43 18.2 GATAC (22%); AACTC (11%); AACAG (11%) GTTAA 9 94 9.1 ATAAC (20%); GTAAC (10%); TTAAT (10%); TAAAC (10%) GTTAC 0 94 0.0 GAAAC (25%); GGAAC (10%); ATAAC (10%); GTAAA (10%) GTTAG 5 52 8.3 ATAAC (27%); CTTAC (18%); GTAAC (9%) GTTAT 14 43 25.0 AGAAC (22%); ATACC (11%); ACAAC (11%) GTTCA 14 80 15.0 GGAAC (24%); TGGAC (18%); TGAAT (12%) GTTCC 14 76 15.8 GGAAA (19%); GAAAC (12%); GGAAT (6%) GTTCG 0 99 0.0 CGACC (24%); AGAAC (10%); CGAAT (10%); CAAAC (10%) GTTCT 14 52 21.4 AGAAT (27%); AAAAC (18%); AGAAA (9%) GTTGA 0 66 0.0 ACAAC (14%); TCAGC (14%); GCAGC (7%); AAAAC (7%) GTTGC 0 43 0.0 ACAAC (22%); GCAGC (11%); GCAAG (11%); GCAAT (11%) GTTGG 9 80 10.5 CCATC (18%); CTGAC (12%); CCGGC (6%) GTTGT 0 47 0.0 ACACC (20%); GCGAC (10%); ACTCC (10%); ACCAC (10%) GTTTA 14 66 17.6 GAAAC (21%); AAAAC (14%); TTAAC (14%) GTTTC 19 85 18.2 GAATC (28%); AAAAC (17%); GTAAC (11%) GTTTG 9 57 14.3 CAACC (17%); ACAAC (8%); AAAAC (8%) GTTTT 9 52 15.4 AAAGC (27%); GAAAC (18%); CAAAC (18%) TAAAA 52 38 57.9 ATTTA (25%); TTTTT (25%); TTATA (25%) TAAAC 14 38 27.3 GTTAA (25%); GGTTA (25%); GTATA (25%) TAAAG 33 85 28.0 CATTA (22%); CTCTA (11%); CTTCA (11%) TAAAT 24 57 29.4 ATTAA (17%); ATTTC (17%); ATTCA (17%) TAACA 28 57 33.3 TGTGA (17%); GGTTA (8%); TGTTC (8%) TAACC 24 76 23.8 GGTCA (19%); GATTA (12%); AGTTA (12%) TAACG 5 109 4.2 CGTTC (13%); CGATA (13%); AGTTA (13%); CGTAA (13%) TAACT 28 28 50.0 AGTTT (33%); AGTGG (17%); GGCTA (17%) TAAGA 47 52 47.6 ACTTA (36%); GCTTA (27%); TCTTG (18%) TAAGC 43 99 30.0 GATTA (19%); GCTTT (19%); ACTTA (10%) TAAGG 28 76 27.3 ACTTA (25%); CCTAA (25%); CCGTA (12%) TAAGT 38 52 42.1 GCTTA (27%); ATTTA (18%); ACTGA (18%) TAATA 71 24 75.0 CATTA (20%); TATTC (20%); AATTA (20%) TAATC 14 52 21.4 GAATA (27%); GATAA (18%); GAGTA (9%) TAATG 9 57 14.3 CAGTA (17%); GATTA (8%); CGTTA (8%) TAATT 47 33 58.8 AATTG (29%); GATTA (14%); AACTA (14%) TACAA 19 14 57.1 GTGTA (33%); TGGTA (33%); CTGTA (33%) TACAC 5 71 6.3 GAGTA (20%); GTGGA (20%); GTGCA (13%); GTGTC (13%) TACAG 14 76 15.8 CTGCA (25%); ATGTA (12%); CTGGA (12%) TACAT 5 57 7.7 ATGCA (25%); ATGGA (25%); AAGTA (17%); GCGTA (8%) TACCA 9 19 33.3 CGGTA (50%); TGATA (25%); TGGAA (25%) TACCC 5 52 8.3 GGGCA (27%); GGGTC (18%); GGGAA (9%); GGTTA (9%) TACCG 14 85 14.3 CGGGA (22%); CGGTC (17%); CGGCA (17%) TACCT 19 66 22.2 AGGGA (21%); AGGAA (21%); TGGTA (14%) TACGA 5 90 5.0 TCGGA (26%); TCGCA (16%); ACGTA (11%); TCGAA (11%) TACGC 9 47 16.7 ACGTA (20%); GCGCG (10%); GGGTA (10%) TACGG 9 57 14.3 CCGGA (25%); CAGTA (17%); TCGTA (17%) TACGT 14 66 17.6 AAGTA (14%); ACGGA (14%); ACGTC (14%) TACTA 19 28 40.0 CAGTA (50%); TAGTT (33%); GAGTA (17%) TACTC 14 80 15.0 AAGTA (29%); GAGAA (18%); CAGTA (12%) TACTG 14 38 27.3 CAGAA (25%); CATTA (25%); CGGTA (12%) TACTT 28 24 54.5 AAGGA (40%); GAGGA (20%); AAGTG (20%) TAGAA 57 28 66.7 GTCTG (33%); TTCCA (33%); TTGTA (17%) TAGAC 5 90 5.0 GCCTA (16%); GTCAA (16%); GACTA (11%); GTCCA (11%) TAGAG 9 85 10.0 CTCTT (22%); CTCTC (11%); ATCTA (11%) TAGAT 19 52 26.7 ATCCA (27%); GTCTA (27%); AACTA (9%) TAGCA 19 76 20.0 AGCTA (31%); TGCCA (19%); TGATA (19%) TAGCC 14 66 17.6 GACTA (14%); GGATA (14%); GGCCG (7%) TAGCG 14 76 15.8 CGCGA (25%); AGCTA (19%); CGCCA (12%) TAGCT 5 33 12.5 AGGTA (29%); AGCAA (14%); AGCTG (14%) TAGGA 43 47 47.4 TCCTG (30%); TCGTA (20%); TCTTA (10%) TAGGC 5 61 7.1 GGCTA (15%); GCCCA (15%); ACCTA (15%) TAGGG 0 33 0.0 CCCTT (29%); CCATA (14%); CACTA (14%); CGCTA (14%) TAGGT 5 80 5.6 GCCTA (18%); ACCGA (18%); ACCAA (12%); AACTA (12%) TAGTA 19 24 44.4 TACGA (40%); TACTT (20%); CACTA (20%) TAGTC 28 71 28.6 GACAA (47%); GACCA (13%); GGCTA (7%) TAGTG 28 57 33.3 CACGA (25%); CACCA (25%); CTCTA (8%) TAGTT 24 52 31.3 TACTA (18%); AACTC (18%); AGCTA (18%) TATAA 43 14 75.0 TTTTA (33%); TTAGA (33%); ATATA (33%) TATAC 24 24 50.0 GTGTA (20%); GTAAA (20%); GTACA (20%) TATAG 28 9 75.0 CTAGA (50%); CTATC (50%) TATAT 52 52 50.0 ATAGA (27%); GTATA (18%); ATTTA (9%) TATCA 38 85 30.8 AGATA (22%); CGATA (17%); TGACA (11%) TATCC 14 57 20.0 AGATA (33%); GAATA (17%); GGAGA (8%) TATCG 28 61 31.6 CGATC (15%); CGATT (15%); CGATG (15%) TATCT 24 52 31.3 TGATA (18%); AGGTA (18%); AGACA (9%) TATGA 24 76 23.8 GCATA (25%); TCGTA (19%); ACATA (12%) TATGC 28 66 30.0 GCATC (14%); GCATT (14%); GCACA (14%) TATGG 14 90 13.6 CCATC (16%); CCATT (11%); CCATG (11%) TATGT 24 52 31.3 ACGTA (18%); ACATC (18%); ACATG (9%) TATTA 71 24 75.0 TAACA (20%); AAATA (20%); GAATA (20%) TATTC 28 43 40.0 GAAAA (22%); GAACA (22%); AAATA (22%) TATTG 14 38 27.3 CTATA (38%); CAAGA (12%); CAAAA (12%) TATTT 57 47 54.5 AAATT (30%); AAATG (20%); AAAGA (10%) TCAAA 52 24 68.8 TTAGA (40%); TTTTA (20%); TTGGA (20%) TCAAC 0 33 0.0 GTGGA (29%); GTAGA (14%); GTTAA (14%); TTTGA (14%) TCAAG 9 71 11.8 CTCGA (20%); CTTCA (13%); CTTAA (13%) TCAAT 28 85 25.0 AATGA (22%); ATGGA (17%); ATTAA (11%) TCACA 9 52 15.4 AGTGA (18%); TGAGA (18%); TGTGG (9%) TCACC 9 61 13.3 GGAGA (23%); GGTAA (23%); GGCGA (15%) TCACG 19 94 16.7 CATGA (25%); CGAGA (15%); CGTTA (10%) TCACT 9 66 12.5 TGTGA (21%); AGAGA (14%); AGTGT (7%) TCAGA 28 47 37.5 TCAGA (40%); GCTGA (20%); ACTGA (20%) TCAGC 0 90 0.0 GCTCA (16%); GCTTA (16%); GCTAA (11%); GCCGA (11%) TCAGG 5 137 3.3 CCTTA (10%); CCAGA (7%); CGTGA (7%); CATGA (7%) TCAGT 33 76 30.4 ACTAA (19%); ATTGA (19%); AATGA (12%) TCATA 24 43 35.7 AATGA (33%); GATGA (22%); CATGA (11%) TCATC 14 57 20.0 GACGA (25%); GAAGA (25%); GAGGA (8%) TCATG 14 76 15.8 CAAGA (19%); CATGC (12%); CAGGA (12%) TCATT 33 76 30.4 AAAGA (19%); AATGT (12%); AACGA (12%) TCCAA 33 38 46.7 TCGGA (38%); ATGGA (25%); CTGGA (25%) TCCAC 5 66 6.7 GAGGA (29%); GCGGA (21%); GTAGA (14%); GTGGC (14%) TCCAG 33 113 22.6 CTGAA (17%); CAGGA (8%); CTGTA (8%) TCCAT 9 61 13.3 AGGGA (15%); ACGGA (15%); GTGGA (15%); AAGGA (15%) TCCCA 24 38 38.5 TGGGC (25%); AGGGA (25%); TGAGA (12%) TCCCC 9 76 11.1 AGGGA (19%); GGGAA (12%); GGGGC (12%) TCCCG 5 104 4.3 CGGAA (27%); CGAGA (14%); CGGGT (14%); CGGTA (14%) TCCCT 14 28 33.3 AGAGA (33%); AGGGC (17%); AGGGT (17%) TCCGA 9 66 12.5 ACGGA (29%); TCGGC (14%); TCGGG (14%) TCCGC 14 123 10.3 ACGGA (35%); TCGGA (15%); GCGGG (12%) TCCGG 19 99 16.0 CAGGA (14%); CGGGA (14%); CCGCA (10%) TCCGT 0 38 0.0 ACGGG (25%); CCGGA (25%); GCGGT (25%); ACGAA (12%) TCCTA 43 28 60.0 CAGGA (33%); TCGGA (17%); GAGGA (17%) TCCTC 5 80 5.6 AAGGA (29%); GAGTA (18%); CAGGA (18%); GAGAA (18%) TCCTG 52 90 36.7 CAGAA (16%); TAGGA (16%); CGGGA (11%) TCCTT 43 66 39.1 CAGGA (21%); AAGGC (14%); AAGGT (7%) TCGAA 57 61 48.0 ATCGA (38%); TACGA (15%); TTTGA (15%) TCGAC 14 113 11.1 ATCGA (25%); GACGA (17%); GTCAA (17%) TCGAG 24 94 20.0 CACGA (20%); CTTGA (15%); CGCGA (10%) TCGAT 9 52 15.4 ACCGA (27%); AGCGA (18%); ATCAG (9%) TCGCA 9 80 10.5 TACGA (18%); TGCAA (18%); AGCGA (18%) TCGCC 14 109 11.5 GGCAA (26%); AGCGA (17%); GACGA (13%) TCGCG 14 128 10.0 CACGA (15%); CGCAA (11%); CGAGA (11%) TCGCT 9 71 11.8 AGCAA (20%); AGTGA (20%); GGCGA (13%) TCGGA 9 137 6.5 TACGA (17%); TCCGC (14%); ACCGA (10%); TCCAA (10%) TCGGC 14 123 10.3 GCCAA (19%); GCCTA (12%); ACCGA (12%) TCGGG 14 109 11.5 CCCAA (17%); CCCCA (13%); CACGA (9%) TCGGT 14 61 18.8 ACCGC (15%); ACCGG (15%); TACGA (8%) TCGTA 5 71 6.3 TATGA (20%); TACGG (13%); TACGT (13%); TAGGA (13%) TCGTC 14 80 15.0 AACGA (24%); GACAA (18%); GCCGA (18%) TCGTG 9 61 13.3 CAGGA (15%); CTCGG (15%); CAACA (8%) TCGTT 38 76 33.3 AACGG (19%); AATGA (12%); AACGC (12%) TCTAA 85 28 75.0 CTAGA (50%); TTAGC (17%); TTAGT (17%) TCTAC 14 52 21.4 GCAGA (18%); CAAGA (9%); GGAGA (9%) TCTAG 24 99 19.2 CAAGA (24%); CGAGA (19%); GTAGA (10%) TCTAT 9 38 20.0 AGAGA (25%); ACAGA (25%); GTAGA (12%) TCTCA 19 47 28.6 AGAGA (20%); TGACA (20%); CGAGA (10%) TCTCC 9 61 13.3 AGAGA (31%); GGTGA (15%); GAAGA (15%) TCTCG 9 19 33.3 CGAGC (25%); TGAGA (25%); AGAGA (25%) TCTCT 5 24 16.7 CGAGA (40%); AGAGG (20%); AGAGT (20%) TCTGA 28 76 27.3 ACAGA (25%); TCGGA (19%); TCAGG (12%) TCTGC 33 104 24.1 ACAGA (41%); CCAGA (14%); GCAGG (9%) TCTGG 38 104 26.7 GCAGA (18%); CCGGA (14%); CTAGA (9%) TCTGT 19 80 19.0 ACAGG (18%); ACGGA (18%); CCAGA (12%) TCTTA 47 43 52.6 CAAGA (44%); GAAGA (11%); TGAGA (11%) TCTTC 19 90 17.4 AAAGA (21%); GAAAA (16%); CAAGA (11%) TCTTG 33 52 38.9 TAAGA (18%); CCAGA (18%); CAATA (18%) TCTTT 24 61 27.8 GAAGA (23%); AAAGG (23%); AAGGA (23%) TGAAA 38 66 36.4 TTACA (36%); CTTCA (14%); ATTCA (14%) TGAAC 14 61 18.8 GTCCA (23%); GATCA (15%); GTTTA (8%) TGAAG 28 76 27.3 CCTCA (19%); CTCCA (12%); ATTCA (12%) TGAAT 38 80 32.0 AATCA (18%); GTTCA (12%); ATTCT (12%) TGACA 28 104 21.4 TGTTA (14%); GGTCA (14%); CGTCA (14%) TGACC 5 90 5.0 GGACA (21%); AGTCA (21%); GGTAA (11%); GATCA (11%) TGACG 0 90 0.0 CGTCC (16%); GGTCA (11%); AGCCA (5%); CGCCA (5%) TGACT 24 61 27.8 AGCCA (15%); AGGCT (15%); AGGCA (15%) TGAGA 19 47 28.6 TCACA (20%); TCTTA (10%); TATCA (10%) TGAGC 14 71 16.7 GATCA (13%); GCACA (13%); GCTGA (13%) TGAGG 24 38 38.5 CCTAA (25%); CCTCC (12%); CCTTA (12%) TGAGT 19 43 30.8 ACACA (11%); ACTTA (11%); ACTCG (11%) TGATA 38 85 30.8 TAGCA (17%); GATCA (17%); TGTCA (11%) TGATC 14 52 21.4 GAACA (27%); AATCA (18%); GATTA (9%) TGATG 5 80 5.6 CCTCA (18%); CATCC (12%); TGTCA (12%); AAGCA (12%) TGATT 14 71 16.7 AATCT (27%); AGTCA (20%); TATCA (7%) TGCAA 38 76 33.3 TCGCA (19%); ATGCA (19%); GTGCA (12%) TGCAC 5 43 10.0 GTACA (22%); GGGCA (22%); GTTCA (11%); CTGCA (11%) TGCAG 9 94 9.1 CCGCA (20%); CAGCA (15%); CTACA (10%) TGCAT 9 52 15.4 TTGCA (18%); ATACA (18%); ATGAA (9%) TGCCA 19 113 14.3 TAGCA (12%); TGGCT (12%); TTGCA (8%) TGCCC 14 99 12.5 GGGTA (14%); GGACA (14%); GAGCA (10%) TGCCG 19 104 15.4 TGGCA (9%); CAGCA (9%); CGGGA (9%) TGCCT 14 61 18.8 TGGCA (23%); AGGTG (15%); AGGCC (15%) TGCGA 9 43 18.2 TCGCG (22%); CCGCA (22%); ACGCA (22%) TGCGC 5 76 5.9 GCGCC (19%); GCTCA (12%); GCGCG (6%); TCACA (6%) TGCGG 9 99 8.7 CGGCA (14%); CCCCA (10%); CCACA (10%) TGCGT 5 38 11.1 AAGCA (25%); ACGGA (25%); ACACA (12%); TCGCA (12%) TGCTA 19 47 28.6 CAGCA (20%); TGGCA (20%); AAGCA (20%) TGCTC 5 76 5.9 GAACA (31%); GAGAA (12%); TAGCA (6%); TCGCA (6%) TGCTG 28 80 26.1 AAGCA (18%); CGGCA (12%); CAGCC (12%) TGCTT 24 43 35.7 AAGTA (22%); GTGCA (11%); ACGCA (11%) TGGAA 19 52 26.7 TTCCC (18%); TGCCA (18%); GTTCA (9%) TGGAC 9 94 9.1 GTTCA (15%); GTCAA (15%); GACCA (15%) TGGAG 5 52 8.3 GTCCA (18%); CTCCC (18%); CTACA (9%); CGCCA (9%) TGGAT 14 57 20.0 ATCCT (25%); AGCCA (17%); ATCCG (17%) TGGCA 19 113 14.3 AGCCA (17%); TGCCT (12%); TGCCG (8%) TGGCC 5 80 5.6 GGCCG (12%); GGTCG (12%); AGCCA (12%); GGACA (12%) TGGCG 5 85 5.3 CACCA (22%); CGGCA (11%); CGCCC (11%); TGCCG (6%) TGGCT 5 61 7.1 TGCCA (23%); AGACA (15%); CGCCA (15%); AGCGA (15%) TGGGA 24 57 29.4 TCCCC (8%); GCTCA (8%); CCCCA (8%) TGGGC 14 80 15.0 GCCAA (12%); GCACA (12%); GCCCG (12%) TGGGG 19 57 25.0 CCACA (25%); CCCCC (17%); CCCGA (8%) TGGGT 14 57 20.0 ACCCT (25%); ACACA (17%); ACCCC (8%) TGGTA 9 80 10.5 TACCG (18%); CACCA (18%); TACCT (12%) TGGTC 9 76 11.1 GAACA (12%); GACTA (12%); GACCT (12%); GCCCA (12%) TGGTG 14 57 20.0 CGCCA (17%); CACCT (17%); CCGCA (8%) TGGTT 14 43 25.0 ATCCA (22%); AAACG (11%); ACCCA (11%) TGTAA 43 47 47.4 TTTCA (30%); CTACA (20%); ATACA (20%) TGTAC 14 71 16.7 GTATA (20%); GCACA (13%); GTGCG (7%) TGTAG 19 71 21.1 CTACT (27%); CTCCA (13%); CAACA (7%) TGTAT 14 47 23.1 ATACT (20%); ATACG (20%); ATACC (10%) TGTCA 28 132 17.6 CGACA (21%); AGACA (18%); GGACA (11%) TGTCC 38 80 32.0 GGACC (24%); GGACT (12%); GCACA (12%) TGTCG 9 47 16.7 CGACC (10%); CAACA (10%); AGACA (10%) TGTCT 28 71 28.6 AGACG (13%); AGAGA (13%); GGACA (13%) TGTGA 9 94 9.1 ACACA (25%); TCACT (15%); GCACA (10%) TGTGC 9 57 14.3 GCACC (17%); GCAGA (17%); GCTCA (8%) TGTGG 14 76 15.8 ACACA (25%); ACACG (19%); CCGCA (12%) TGTGT 14 28 33.3 ACATA (33%); GCACA (17%); ACACG (17%) TGTTA 28 47 37.5 GAACA (30%); TGACA (30%); GGACA (10%) TGTTC 28 61 31.6 GGACA (23%); GAACC (15%); AAACA (8%) TGTTG 19 38 33.3 CTACA (25%); CAAGA (12%); CGGCA (12%) TGTTT 9 57 14.3 AGACA (17%); AAACC (17%); AAACG (8%) TTAAA 52 14 78.6 TTCAA (33%); TTTAG (33%); TTGAA (33%) TTAAC 9 43 18.2 GTTTA (22%); TTTAA (22%); GCTAA (11%) TTAAG 24 38 38.5 ATTAA (12%); CTCAA (12%); CTTTA (12%) TTAAT 38 28 57.1 GTTAA (33%); ATTAG (17%); TTTAA (17%) TTACA 43 66 39.1 TGAAA (36%); TGCAA (14%); TGTCA (14%) TTACC 19 85 18.2 GGCAA (22%); GGTAT (17%); AGTAA (17%) TTACG 19 90 17.4 AGTAA (21%); CGAAA (16%); CGCAA (11%) TTACT 0 47 0.0 AGAAA (30%); AGGAA (20%); GTTAA (10%); AGTAC (10%) TTAGA 85 80 51.4 TTTAA (18%); CCTAA (18%); GCTAA (12%) TTAGC 9 76 11.1 ACTAA (12%); GCTAG (12%); GCCAA (12%) TTAGG 5 71 6.3 CCGAA (20%); CCTAT (13%); CCAAA (13%); CCTCA (13%) TTAGT 19 47 28.6 ACGAA (30%); GCTAA (20%); TCTAA (10%) TTATA 43 28 60.0 TAAAA (33%); TAGAA (17%); TATCA (17%) TTATC 38 57 40.0 GAGAA (17%); GCTAA (8%); GAAAA (8%) TTATG 33 47 41.2 CATAG (20%); CATGT (10%); CATAC (10%) TTATT 43 24 64.3 AATTA (20%); AAGAA (20%); AATAT (20%) TTCAA 80 24 77.3 TTGGA (40%); TTAAA (20%); ATGAA (20%) TTCAC 24 43 35.7 GAGAA (56%); GGGAA (11%); GTCAA (11%) TTCAG 33 104 24.1 CAGAA (27%); CCGAA (14%); CTGAT (14%) TTCAT 43 43 50.0 ACGAA (33%); AAGAA (22%); ATGGG (11%) TTCCA 19 43 30.8 CGGAA (33%); TAGAA (22%); AGGAA (22%) TTCCC 24 47 33.3 TGGAA (20%); GGAGA (10%); GCGAA (10%) TTCCG 14 76 15.8 CCGAA (12%); CGGAG (12%); CGGAC (12%) TTCCT 5 19 20.0 CGGAA (25%); AAGAA (25%); AGGTA (25%) TTCGA 57 113 33.3 ACGAA (29%); CCGAA (21%); GCGAA (12%) TTCGC 5 80 5.6 ACGAA (29%); GAGAA (24%); CCGAA (12%); GCAAA (12%) TTCGG 5 61 7.1 CAGAA (15%); CCGGA (15%); CCCAA (8%) TTCGT 19 38 33.3 ACGAG (38%); CCGAA (25%); ACGTA (25%) TTCTA 57 28 66.7 AAGAA (33%); GAGAA (33%); CAGAA (17%) TTCTC 9 47 16.7 CAGAA (20%); GAGGA (20%); GGGAA (10%) TTCTG 14 71 16.7 CTGAA (20%); CGGAA (20%); CAGAT (20%) TTCTT 43 52 45.0 GAGAA (36%); AAGTA (27%); AAGAG (9%) TTGAA 80 19 81.0 TTAAA (25%); GTCAA (25%); ATCAA (25%) TTGAC 14 76 15.8 GCCAA (19%); ATCAA (19%); GGCAA (19%) TTGAG 24 61 27.8 CTCAT (23%); CTCTA (15%); CCCAA (15%) TTGAT 14 14 50.0 ATCGA (67%); GTCAA (33%) TTGCA 38 85 30.8 AGCAA (22%); CGCAA (17%); GGCAA (17%) TTGCC 5 66 6.7 GGCTA (14%); GGCAT (14%); GTCAA (14%); CGCAA (14%) TTGCG 5 61 7.1 CCCAA (15%); TGCAA (15%); CGCTA (15%); CTCAT (8%) TTGCT 9 52 15.4 AGCTA (18%); AGCGA (18%); AGCAG (18%) TTGGA 33 66 33.3 GCCAA (21%); ACCAA (21%); TTCAA (14%) TTGGC 5 99 4.5 GCCAT (14%); GGCAA (14%); CCCAA (10%); GCCTA (10%) TTGGG 9 38 20.0 CCCGT (12%); CCCAT (12%); CCCGA (12%) TTGGT 14 43 25.0 ACCGA (33%); ACAAA (11%); ACTAA (11%) TTGTA 19 47 28.6 GACAA (20%); TACAG (20%); CACAA (20%) TTGTC 24 80 22.7 GACTA (18%); GCCAA (12%); GATAA (12%) TTGTG 5 57 7.7 CGCAA (17%); TACGA (8%); CACGA (8%); CAAAA (8%) TTGTT 5 47 9.1 AACCA (20%); GACAA (20%); AACAG (20%); AACGA (20%) TTTAA 52 47 52.4 TTAGA (30%); CTAAA (20%); TTAAC (20%) TTTAC 38 52 42.1 GGAAA (27%); GTAGA (18%); GTCAA (18%) TTTAG 28 66 30.0 ATAAA (14%); CTGAA (14%); GTAAA (14%) TTTAT 24 47 33.3 GTAAA (30%); ATAAG (20%); AGAAA (20%) TTTCA 38 43 47.1 TGTAA (33%); GGAAA (22%); TGAAG (11%) TTTCC 43 38 52.9 GGAGA (38%); GGAAG (25%); AGAAA (25%) TTTCG 28 66 30.0 CGATA (29%); CGAAT (21%); AGAAA (14%) TTTCT 19 43 30.8 GGAAA (44%); TGAAA (11%); AGAAT (11%) TTTGA 52 57 47.8 ACAAA (33%); TCGAA (17%); GCAAA (17%) TTTGC 14 52 21.4 GCATA (18%); GCAGA (18%); GAAAA (9%) TTTGG 5 38 11.1 ACAAA (12%); CCGAA (12%); CCAAT (12%); CGAAA (12%) TTTGT 19 28 40.0 ACAAT (17%); ACATA (17%); ACTAA (17%) TTTTA 52 24 68.8 GAAAA (40%); TATAA (20%); TCAAA (20%) TTTTC 28 61 31.6 GTAAA (15%); GGAAA (15%); GAATA (15%) TTTTG 19 52 26.7 CGAAA (27%); CAAAG (18%); CAAGA (9%) TTTTT 24 28 45.5 TAAAA (33%); AAAAG (17%); GAAAA (17%) ¹Fidelity is calculated as the fraction of correct ligations divided by the total fraction of ligations for a given overhang. ²Top 3 or 4 mismatch overhangs are given for each overhang. All overhangs are written in the 5′-to-3′ direction. The numbers in parenthesis give the percentage for the given mismatch ligation relative to the total number of mismatch ligations for the overhang.

Example 2: Use of Ligation Fidelity Tables

Example 1 describes how to generate comprehensive ligation fidelity data for all overhang sequences for a given overhang length, using a specific ligase at a specific reaction temperature. Data tables are 16×16 (2-base), 64×64 (3-base) 256×256 (4-base), ×1024×1024 (5-base), 4096×4096 (6-base), etc. The ligation fidelity tables permit testing of substrates that simultaneously measure net effect of cutting, melting, annealing, and ligation for a particular combination of Type IIS restriction enzyme and DNA ligase under a given set of cycling conditions. Relative efficiency and fidelity of every overhang pairing is thus obtained. These data sets allow selection of Watson Crick pairs that ligate with their own partner efficiently but include no overhangs that can form ligation products with any partners containing one or more mismatches. For a given set of conditions, a computer can provide a user an output containing the highest fidelity set with good efficiency for any chosen number of junctions (10 junction pairs, 12 junction pairs, 15 junction pairs, 20 junction pairs, etc.). More pairs mean lower maximal fidelity. If a desired set of junctions have already been selected, the computer can process multiple data sets (for multiple ligases, restriction enzymes, cycling conditions) to choose the set of enzymes and reaction conditions that would give the highest possible fidelity and efficiency for the set of overhangs chosen. Intermediate cases are possible. Some overhangs and some reaction parameters could be defined by the user, while the computer output provided additional overhangs and reaction conditions to give the best efficiency and fidelity possible for the needed number of connections using the data sets that have been experimentally derived.

Users could also provide a gene, gene pathway, plasmid or chromosome sequence and specify it be divided into fragments that could be used to assemble that sequence efficiently with high fidelity. The user could specify the number of fragments, and the algorithm could then divide the master sequence into that number of fragments at the best set of junctions as above. The user could specify the minimum acceptable fidelity and the program could divide the sequence into the maximum number of sequences possible with junctions that provide that fidelity or better.

Example: 3: Selection of Parameters in Addition to the Sequence of Overhangs Desirable for Ordered Assembly of a Target Nucleic Acid from a Large Number of Polynucleotides

Ligation Protocols Relating to Temperature

A set of parameters were tested that related to the temperature at which ligation occurred. Ligation reactions were carried using three different protocols. These were (i) static ligation at a fixed temperature; (ii) drop-down ligation that involved cycling between a high temperature and a low temperature (e.g., 30 cycles of 10 minutes each for a total of 5 hours between 37° C. and 16° C.); (iii) touch-down ligation that involved 30 cycles from a high temperature to a low temperature in evenly divided incremental steps in descending order. For example, 30 cycles between a high temperature of 37° C. and a low temperature of 16° C. over 5 hours meant cycling between a step down in temperature in each cycle of a cumulative 0.7° C. followed by a fixed increase to the maximum temperature (37° C.) each for a prescribed time period of 5 minutes (total incubation time/60 cycles). For example, the first cycle would be 37° C. to 36.3° C. to 37° C. (1 cycle) to 35.6° C. to 37° C. and so on for a 21° C. decrease over 30 cycles until the last cycle is 37° C. to 16° C. completed within a 5-hour incubation; and (iv) touch-up ligation. This ligation protocol is the reverse of touch-down starting at the lowest temperature and incrementally cycling to the highest temperature (e.g., 16° C./37° C.). Various upper range temperatures from 37° C. to 50° C. were tested using various ligases and restriction endonucleases and static, drop-down or touch-down incubation conditions.

In detail, the ligation conditions tested are listed below:

-   -   (a) Ligation conditions for wt T4 DNA ligase:

For static ligation at a fixed temperature where the ligation reaction was performed at 37° C., 45° C. and 50° C. for 2 fragments with 4-base overhangs over 16 hours and for assembly of large numbers of DNA fragments for extended periods (such as greater than 24 hours) preferably at 37° C.; (ii) ligation under drop-down conditions where the ligation reaction was performed first at 37° C. and then at 16° C. over 5 hours for 30 cycles between the high and the low temperature for joining 2 fragments, 12 fragments and 24 fragments with 4-base overhangs and 2 fragments with 3-base overhangs. Drop-down cycling for 30 cycles was also performed between 50° C. and 16° C. for joining 10 fragment with 3-base overhangs over 16 hours and for joining 52 fragments over 24 hours with 4-base overhangs and cycling between 42° C. and 16° C. for joining 24 and 52 fragments over 5 hours with 4-base overhangs; (iii) ligation under touch-down cycling conditions in which the temperature was cycled in increments from 37° C. for 5 minutes in increments of 0.7° C./cycle at each temperature until a temperature of 16° C. was reached after 30 cycles.

It was found with wt T4 DNA ligase could tolerate a drop-down cycling protocol between 42° C. and 16° C. for less than 24 hours producing ordered assemblies that were visible as blue colonies at these temperatures. In Table 8, no colonies were detected with wt T4 DNA polymerase at cycling temperatures of 50° C./16° C.

-   -   (b) Ligation conditions for a thermostable variant of T4 DNA         ligase (Hi-T4 DNA ligase, New England Biolabs, Ipswich, Mass.)     -   Ligation reactions were carried using three different protocols.         These were (i) static; (ii) drop-down; (iii) touch-down;         and (iv) touch-up.     -   (c) Static (at 37° C., 45° C. or 50° C. for 16 hours (2         fragments with 4-base overhang or 37° C. for >24 hours) or 37°         C.-50° C. or 45° C.-50° C. for long incubation times for         assembly of large numbers of fragments (e.g. 100         fragments); (ii) drop-down; (37° C./16° C., 40° C./16° C., 42°         C./16° C., 45° C./16° C.°, 47° C./16° C., or 50° C./16° C.) for         5 hours (24 fragments with 4-base overhangs) or 50916° for 16         hours (10 fragments with 3-base overhangs) and (iii) touch-down         (37° C./16° C. and 45° C./16° C. for 5 hours for 12 fragments         with 4-base overhangs) and 42° C./16° C. and 50° C./16° C. for         24 hours for 52 fragments with 4-base overhangs.

The use of thermostable T4 DNA ligase variant permitted the elevated upper range cycling temperatures (37° C. to 50° C.) to achieve successful ordered assembly of fragments. The higher the temperature in this range, the greater the accuracy of the ordered assembly of polynucleotide fragments with 4-base overhangs regardless of the restriction endonuclease used with the ligase. Indeed, this benefit was observed with Bsal-HFv2 which is a restriction endonuclease that generally works well at 37° C. BspQl and BsmBl are restriction endonucleases that generally have a preference for a temperature above 37° C. and improved fidelity was also observed with these enzymes at higher upper range temperatures. Depending on the cycling temperatures selected, different restriction endonucleases may be selected for greater assembly efficiency. For example, Esp3l is an isoschizomer of BsmBl. Esp3l prefers a reaction temperature of 37° C. while BsmBl prefers higher temperatures e.g., 45° C., 50° C. or 55° C. Yield was enhanced using a thermostable T4 DNA polymerase compared with wt DNA polymerase. Ratios of restriction endonuclease to ligase were within the range of 1:10-1:1000 regardless of the type of ligase or restriction endonuclease (including BspQl, BsmBl, Hgal, and Bsal-HFv2).

High salt T4 DNA ligase (Salt-T4™, New England Biolabs, Ipswich, Mass.) enabled an ordered assembly of fragments to occur in a high salt buffer where the restriction endonucleases that favor high salt were able to work optimally. This was demonstrated for BsmB1 using 100 mM salt in a 5-hour incubation using a 4-base overhang on 24 fragments with a drop-down temperature of 42° C./16° C.

Of particular note was the successful 52 fragment ordered assembly of a target polynucleotide using touch-down ligation conditions of 50° C./16° C. where the fragments had 4-base overhangs and the one pot enzyme reaction occurred over 24 hours.

Generally, it was found that the addition of EndoMS repair enzyme reduced the background caused by incorrect assemblies.

In summary, various ligation conditions were tested for ordered assembly of various numbers of polynucleotides (2-52) having 3-base and 4-base overhangs. Additional parameters included the length of the incubation, the amount of ligase and restriction endonuclease, the use of three different ligases: wt T4 DNA ligase; thermostable T4 DNA ligase variant; and a high salt T4 DNA ligase variant and the use of different restriction endonucleases: Bsa-HFv2, BsmBl, BspQl, PaqCl and the use of a repair enzyme (EndoMS). The results are summarized in Table 8 in which yield, fidelity and efficiency was determined for each combination of parameters tested.

Example 4: Experimental Protocol for Testing the Above Parameters to Determine Yield, Efficiency, and Fidelity. Ordered Assembly and Cloning of Lac Cassettes (12, 24 and 52 Fragments) and Virus Genomes (10, 24 and 52 Fragments)

In reactions described in Table 8 as specified, ordered assembly reactions consisted of precloned DNA fragments (3 nM each), PCR fragments (3 nM each), or chemically synthesized fragments (100 nM total) and the indicated amount of restriction enzyme and ligase in T4 DNA ligase buffer or a standard restriction endonuclease buffer e.g., CutSmart® buffer (New England Biolabs, Ipswich, Mass.). Assembly reactions were incubated as described above using one of the four different ligation protocols, followed by a 5 minute final incubation step at 60° C. then a final 4° C. hold prior to transformation. Transformations were performed using 2 μl of each assembly reaction added to 50 μl competent T7 Express chemically competent E. coli (New England Biolabs, Ipswich, Mass.) plated on the appropriate growth media, and incubated at 37° C. to form colonies or plaques if the assembled poly nucleotide was an intact phage. Electroporation was used to introduce assembled phage DNA into E. coli. The correctly assembled target polynucleotide coded for the lac operon (about 5 kb) so that blue colonies of correctly assembled fragments could be distinguished from white colonies containing incorrect assemblies on IPTG/Xgal/Chloramphenicol plate.

Colonies were imaged and counted using the aCOLyte 3 automated colony counting system (Synbiosis, Cambridge, UK) or by hand. For each assembly type, total transformants and percentage correct assemblies (blue colonies) were reported as the average result of at least three independent assembly reaction replicates, with the reported error one standard deviation from the mean.

Bacteria containing the correct assembly of the target polynucleotide could be visually identified as blue colonies on the plate versus white colonies which were identified as incorrect assemblies. In the case of phage assembly, since lysis was the end point, it was not possible to obtain fidelity measurements as a ratio of correct/total assemblies. Instead, plaques were identified to provide a measure of yield of correct assemblies.

For viral DNA assembly, a plaque was presumed to be evidence of a successful assembly. Plaques were observed against the lawn of bacteria evenly covering the plate. (In Table 8, Enterobacteria T7 phage genome was successfully assembled from 10 fragments using BspQl or 52 fragments using BsmBl and wt T4 DNA ligase or a thermostable T4 DNA ligase).

Accuracy was determined by sequence analysis of 2 fragment assemblies that were inserted into a SMRT Bell configuration for sequencing.

Selection of Overhang Length

Overhang lengths selection was subjected to at least one of the following parameters:

-   -   availability of enzymes that can generate a chosen overhang         length;     -   number of fragments needed where longer overhangs allow for more         possible fragments;     -   desired efficiency of ligation (longer overhangs ligate more         efficiently);     -   desired efficiency of melting/annealing (shorter overhangs melt         and anneal faster where longer overhangs require higher melting         temperatures).

TABLE 7 Examples of computer-generated optimized overhang sets according to the methods herein. #over- Overhang sequences-one Set hangs sequence/pair is shown. 1 10 AAC, ACT, AGA, ATA, CAA, CCA, CGA, CTC, GCA, GCC 2 12 GGAG, GGTC, AGCA, CAGT, GGTA, GAAT, GGTT, TCTT, GGTG, GCAC, AGCG, GTCT, CCAT 3 15 TGCC, GCAA, ACTA, TTAC, CAGA, TGTG, GAGC, AGGA, ATTC, CGAA, ATAG, AAGG, AACT, AAAA, ACCG 4 20 AGTG, CAGG, ACTC, AAAA, AGAC, CGAA, ATAG, AACC, TACA, TAGA, ATGC, GATA, CTCC, GTAA, CTGA, ACAA, AGGA, ATTA, ACCG, GCGA 5 24 GGAG, GATA, GGCA, GGTC, TCGC, GAGG, CAGT, GTAA, TCCA, CACA, GAAT, ATAG, AGTA, ATCA, TCTT, AGGT, CAAA, AAGC, GCAC, CAAC, CGAA, GTCT, TCAG, CCAT 6 24 GGAG, GATA, GGCA, GGTC, TCGC, GAGG, CAGT, GTAA, TCCA, CACA, GAAT, ATAG, AGTA, ATCA, TCTT, AGGT, CAAA, AAGC, GCAC, CAAC, CGAA, GTCT, TCAG, CCAT 7 24 TTGC, TGGA, TGAG, TAGG, ACAG, AAGC, AGCC, GTCA, CGTT, ATTT, TTCT, GAAA, GATG, GTAT, GCAC, TCGT, GGTC, CGGG, CACT, ACTA, ACCT, TCTC, ATGG, GTAG 8 25 GCCC, CCAA, ATCC, GGTA, ACGG, AAAT, ATAG, CTTA, AGGA, AGTC, ACAC, ATGA, GCGA, CATA, CTGC, AACG, CGCC, AGTG, CCTC, GAAA, CAGA, ACCA, AAGT, CGAA, CAAC 9 30 AAAC, AACA, AAGA, AAGT, AATG, ACAC, ACGA, AGAA, AGCC, AGGG, AGTA, ATAG, ATCA, ATGA, ATTC, CAAA, CACG, CAGA, CCAG, CCTA, CGAA, CGGC, CTCC, CTTA, GAGC, GATA, GCAA, GGGA, GTAA, TCCA 10 52 GGAG, CCAG, ATGT, TACA, GGCA, TATC, TAAG, CAGC, GAAC, CAAC, GCTT, TAGT, CTAT, GGAA, TTCG, AGAC, GTAT, GCGT, GATT, TTAC, TATT, TCGT, CAGA, GGGA, CTCA, GCAA, TGGA, CGTC, AACC, AGTA, TAGA, GAAA, AGGG, TTCT, ACAA, AGGT, TGTT, GAGT, TGGC, ACCG, ATTA, GTGC, AGCG, TCTT, CGTG, CCGA, ATCA, TCTC, CAAA, TTCA, TAGG, TATG, CCAT 11 52 AAAT, AGAA, AGCG, ATGT, TAGT, TCGC, CTGG, ACAA, AGAC, GCTG, GGCA, ACCC, ACCG, AAGC, TACT, AATC, AAGG, GAAA, GGTT, CAAC, CGTC, CCTA, TGGG, TAAG, TCAT, ACGG, GTAA, CATT, TATC, TGAG, GCAC, CCAC, TTCG, TCTG, AGGA, ACGC, TGGC, GTAT, CGTG, CTAT, GAGA, ACTC, GGTG, TCCA, GGGA, GTTC, TTGC, GAAG, GGAA, CAAA, ATCA, TGTT 12 100 TTAC, CCCA, AACT, TTTT, TGTA, CGAA, GGAG, TAGC, CAAG, ACAA, CTAT, GGTC, TGGC, AGAA, ACTT, AGTG, TCTG, ATGC, AAGG, CAAC, TCTT, GAAG, GTGG, TTGA, TCGG, CTCT, GGTA, GATG, AATC, GACA, ACTA, CGCA, TGAA, ATCG, CCAA, CCAT, CATA, GAGA, TAGA, TCGT, GGTT, CTCG, AAAG, GGAT, TGCT, TATT, CTCA, ATTC, TGAT, CATT, CTGG, GTTA, CTAA, AACG, GTAG, ACGC, TGTG, GCAC, GCAA, ATTT, GGCT, TCCG, CTGC, TCAC, TCAT, TAGG, CCGT, GATA, AGAC, TAAG, TCCC, GGGT, GAGT, ATAC, GTTT, TCCA, ACCG, ACTG, CAAA, GGCG, GACT, TGTT, GAAA, TACG, TCAG, GTTC, GCGA, GCTT, GCTC, TACT, AGAT, TGGT, AGGA, TAAT, GGAA, ACCT, CAAT, CCCC, ATGT, TGAC

Overhangs were generated as described above using Bsal-HFv2, BsmBl or BspQl:

The following are the overhangs used in Table 8. Overhangs are written here in the 5′ to 3′ direction with the phosphate omitted.

2-Fragment:

All possible combination of 4-base or 3-base overhangs were tested on 50-base synthetic DNA fragments to create the ligation frequency tables. 10-Fragment Phage Assembly: 3-base overhang (BspQl):

Overhangs: AAC, ACT, AGA, ATA, CAA, CCA, CGA, CTC, GCA, GCC

12-Fragment Lac Assembly: 4-base overhang (Bsal-HFv2):

Overhangs: GGAG, GGTC, AGCA, CAGT, GGTA, GAAT, GGTT, TCTT, GGTG, GCAC, AGCG, GTCT, CCAT

-   -   (Fragment sizes (base pairs): 351, 395, 369, 381, 526, 507, 425,         456, 487, 306, 322, 322)         24-Fragment Lac Assembly: 4-base overhang (Bsal-HFv2; BsmBl):

Overhangs: GGAG, GATA, GGCA, GGTC, TCGC, GAGG, CAGT, GTAA, TCCA, CACA, GAAT, ATAG, AGTA, ATCA, TCTT, AGGT, CAAA, AAGC, GCAC, CAAC, CGAA, GTCT, TCAG, CCAT

-   -   (Fragment sizes (base pairs): 118, 222, 222, 199, 137, 217, 197,         244, 293, 173, 127, 208, 287, 310, 291, 259, 176, 217, 135, 176,         184, 133, 203, 119)

24-Fragment T4 Phage Assembly (BsmBl): Overhangs: GGAG, GATA, GGCA, GGTC, TCGC, GAGG, CAGT, GTAA, TCCA, CACA, GAAT, ATAG, AGTA, ATCA, TCTT, AGGT, CAAA, AAGC, GCAC, CAAC, CGAA, GTCT, TCAG, CCAT

-   -   (Fragment size: 8 kb)

24-Fragment T4 Phage Assembly (BsmBl): Overhangs: TTGC, TGGA, TGAG, TAGG, ACAG, AAGC, AGCC, GTCA, CGTT, AM, TTCT, GAAA, GATG, GTAT, GCAC, TCGT, GGTC, CGGG, CACT, ACTA, ACCT, TCTC, ATGG, GTAG

-   -   (Fragment sizes (base pairs): 4631, 9473, 7031, 7465, 10181,         1595, 8807, 3851, 4152, 10945, 11254, 7290, 1680, 10213, 7152,         6898, 7162, 7104, 6967, 6827, 8052, 8947, 4304, 7018)         30-Fragment All-Purpose Overhang Set (Any 4-cutter):

Overhangs: AAAC, AACA, AAGA, AAGT, AATG, ACAC, ACGA, AGAA, AGCC, AGGG, AGTA, ATAG, ATCA, ATGA, ATTC, CAAA, CACG, CAGA, CCAG, CCTA, CGAA, CGGC, CTCC, CTTA, GAGC, GATA, GCAA, GGGA, GTAA, TCCA

52-Fragment Lac Assembly: 4-base overhang (Bsal-HFv2):

Overhangs:

GGAG, CCAG, ATGT, TACA, GGCA, TATC, TAAG, CAGC, GAAC, CAAC, GCTT, TAGT, CTAT, GGAA, TTCG, AGAC, GTAT, GCGT, GATT, TTAC, TATT, TCGT, CAGA, GGGA, CTCA, GCAA, TGGA, CGTC, AACC, AGTA, TAGA, GAAA, AGGG, TTCT, ACAA, AGGT, TGTT, GAGT, TGGC, ACCG, ATTA, GTGC, AGCG, TCTT, CGTG, CCGA, ATCA, TCTC, CAAA, TTCA, TAGG, TATG, CCAT

-   -   (Fragment sizes (base pairs): 83, 125, 103, 45, 114, 83, 122,         81, 89, 139, 81, 119, 62, 96, 92, 92, 107, 113, 85, 82, 113, 95,         110, 78, 96, 78, 101, 103, 115, 75, 113, 98, 115, 63, 99, 126,         93, 69, 102, 86, 139, 56, 121, 73, 128, 110, 67, 93, 144, 90,         96, 77)

52-Fragment T7 Phage Assembly (BsmBl) Overhangs:

AAAT, AGAA, AGCG, ATGT, TAGT, TCGC, CTGG, ACAA, AGAC, GCTG, GGCA, ACCC, ACCG, AAGC, TACT, AATC, AAGG, GAAA, GGTT, CAAC, CGTC, CCTA, TGGG, TAAG, TCAT, ACGG, GTAA, CATT, TATC, TGAG, GCAC, CCAC, TTCG, TCTG, AGGA, ACGC, TGGC, GTAT, CGTG, CTAT, GAGA, ACTC, GGTG, TCCA, GGGA, GTTC, TTGC, GAAG, GGAA, CAAA, ATCA, TGTT

-   -   (Fragment sizes (base pairs): 779, 918, 512, 465, 810, 756, 731,         820, 690, 759, 813, 743, 644, 1043, 494, 887, 526, 918, 854,         837, 540, 880, 678, 812, 732, 802, 976, 530, 745, 568, 885,         1130, 148, 1008, 847, 667, 748, 831, 842, 753, 947, 428, 928,         411, 301, 1383, 424, 1056, 893, 653, 815, 1735)

100-Fragment T4 Phage Assembly (BsmBl): Overhangs:

TTAC, CCCA, AACT, TTTT, TGTA, CGAA, GGAG, TAGC, CAAG, ACAA, CTAT, GGTC, TGGC, AGAA, ACTT, AGTG, TCTG, ATGC, AAGG, CAAC, TCTT, GAAG, GTGG, TTGA, TCGG, CTCT, GGTA, GATG, AATC, GACA, ACTA, CGCA, TGAA, ATCG, CCAA, CCAT, CATA, GAGA, TAGA, TCGT, GGTT, CTCG, AAAG, GGAT, TGCT, TATT, CTCA, ATTC, TGAT, CATT, CTGG, GTTA, CTAA, AACG, GTAG, ACGC, TGTG, GCAC, GCAA, ATTT, GGCT, TCCG, CTGC, TCAC, TCAT, TAGG, CCGT, GATA, AGAC, TAAG, TCCC, GGGT, GAGT, ATAC, GTTT, TCCA, ACCG, ACTG, CAAA, GGCG, GACT, TGTT, GAAA, TACG, TCAG, GTTC, GCGA, GCTT, GCTC, TACT, AGAT, TGGT, AGGA, TAAT, GGAA, ACCT, CAAT, CCCC, ATGT, TGAC

-   -   (Fragment sizes (base pairs): 395, 383, 424, 367, 451, 506, 287,         411, 352, 355, 419, 357, 519, 208, 448, 379, 412, 380, 422, 475,         337, 481, 242, 537, 320, 450, 522, 149, 562, 329, 312, 567, 389,         328, 456, 301, 390, 479, 282, 402, 494, 340, 450, 287, 569, 380,         396, 334, 390, 412, 295, 487, 199, 627, 290, 557, 382, 409, 296,         418, 906, 143, 193, 296, 436, 412, 465, 295, 511, 312, 341, 369,         448, 451, 421, 297, 380, 425, 479, 150, 679, 320, 356, 495, 223,         562, 399, 319, 317, 268, 628, 435, 368, 355, 451, 308, 555, 336,         357, 1074)

Choice of Ligase

A ligase can be selected that has been optimized for the ordered assembly of a particular set of polynucleotide fragments. This can depend on temperature and salt tolerance for optimizing function with a selected restriction endonuclease. Various ligases may have a preference for the length of overhang preferring Watson-Crick pairs to pairings with one or more mismatch to produce a high-fidelity product. Other factors may include the number of fragments to be joined and the length of the incubation period required to produce fragments by restriction endonuclease cleavage and to ligate the fragments together with a shared preference by the endonuclease and ligase for buffers and cycling conditions.

An example of a ligase that is suitable for high temperature ligation (greater than 42° C.) and meets minimum criteria for fidelity, efficiency and yield of assembled fragments includes a high temperature mutant of T4 DNA ligase. An example of a ligase that is capable of functioning at high salt concentrations favored by selected Type IIS bacillus restriction endonucleases for efficient cleavage, includes a salt tolerant mutant of T4 DNA Ligase.

Other ligases that are naturally occurring or variants of naturally occurring ligases may include those derived from extremophiles that naturally survive at high temperatures such as archaeal ligases or derived from bacteria that flourish in high salt environments or ligase encoded by the phage that parasitize these organisms. Other phage ligases may be selected that can ligate overhangs containing modified nucleotides that may be desirable in some cases.

The Restriction Endonuclease

A Type IIS restriction endonuclease can be selected that efficiently cleaves DNA outside its recognition sequence to create a 3-base, 4-base or 5-base overhang. Examples of endonucleases that are capable of cleaving a 3-base overhang are BspQl and Sapl. Examples of endonucleases that are capable of cleaving a 4-base overhang include BsmBl, Bsal-HFv2 and Bsal and an example of an endonuclease that is capable of creating a 5-base overhang is Hgal. One feature that differentiates various Type IIS restriction endonucleases having the same number of bases in the overhang is the number of bases in the recognition sequence. For example, the Bbsl family has a 6 nucleotide recognition sequence with a 4-base overhang whereas the Aarl family has a 7 nucleotide recognition sequence with a 4-base overhang. The benefit of a longer recognition sequence is that this reduces the likelihood of internal cleavage sites in fragments that have been selected for joining. Experiments have shown that the longer overhangs (5-base overhangs) result in lower fidelity in joined fragments compared with 3 and 4-base overhangs. Moreover, restriction endonucleases may vary in their activity. While Aarl has the desired characteristics of a 7-base recognition sequence and 4-base overhang, PaqCl has been found here to be a more active endonuclease and therefore more suitable for DNA assembly reactions.

All of the Type IIS enzymes described herein are commercially available from New England Biolabs, Ipswich, Mass. The unit definition for Hi-T4 and Salt-T4® ligase (New England Biolabs, Ipswich, Mass.) are the same as wt T4 DNA ligase (one unit is defined as the amount of enzyme required to give 50% ligation of HindIII fragments of λ DNA (5′ DNA termini concentration of 0.12 μM, 300-μg/ml) in a total reaction volume of 20 μl in 30 minutes at 16° C. in 1×T4 DNA Ligase Reaction Buffer.

The results of assembly reactions using a variety of fragments and of parameters is provided in Table 8.

Example 5: Using the Client, Server and Data Base to Design an Assembly of a Large DNA

(A) Whole bacteriophage genomes can be assembled with at least 50% ligation assembly fidelity using 50 polynucleotide fragments having 4-base overhangs that are formed as products of Bsal-HFv2 cleavage using the computer system described herein.

(B) Whole chloroplast genomes can be assembled with at least 20% assembly fidelity using 100 polynucleotide fragments having 4-base overhangs that are formed as products of Bsal-HFv2 cleavage using the computer system described herein.

(C) Assembly of a termite ligase capable of digesting lignin efficiently and a termite metabolic pathway for achieving the same with at least 20% assembly fidelity comprising selecting polynucleotide fragments with 4-base overhangs derived from the termite genome for assembly into a target nucleic acid.

In the above cases, the user inputs a Genome sequence into the computer. The computer checks potential insert sequences for internal Bsal-HFv2 sites (or other Type IIS recognition sites according to choice of enzyme). The computer processes the sequences using a database of overhang ligation efficiencies under various experimental conditions and using selected components where the selection is performed by the computer, the user or both in part. The computer outputs a genomic sequence with suggested break points. If these breakpoints are accepted by the user, the computer outputs a set of primer designs to introduce a Type IIS restriction site adjacent to a sequence that can form a unique 4-base overhang. The primers feature 6-bases at the 5″-end flanking the Bsal-HFv2 recognition site, the recognition site itself, plus the 4-base unique overhangs separated from the recognition site by N1 base and determine correct annealing and ligation of the inserts. All overhangs output by the computer are non-palindromic (to eliminate self-insert ligations), unique, and in the correct orientations to ensure correct assembly. The polynucleotides corresponding to the fragments output are synthesized and amplified as needed using the primers to form amplicons that can be purified. Alternatively, polynucleotide fragments can be cloned as inserts into plasmids (see FIG. 2A-2C). Amplicons or precloned inserts can then be treated with a Type IIS restriction enzyme (e.g., Bsal-HFv2) and a ligase (e.g., T4 DNA ligase) in a single reaction and incubated under predetermined experimental conditions where these have been optimized by the computer or selected by the user. With optimized buffer components and enzyme ratios, a single reaction containing a destination plasmid such as pGGA and inserts (PCR amplicons or precloned) will result in ligation of inserts with complementary cohesive ends and the accumulation of assembled product (target nucleic acid) as a function of time. The final assembly has no Bsal-HFv2 recognition sites, rendering the assembly inert to further digestion by Bsal-HFv2. The product of the reaction is a target nucleic acid which can introduced into a destination vector for transformation into a bacterial cell and cloned on selective media (see for example FIG. 3A-3C). Precloning is recommended for inserts of size greater than 3 kb or those containing repetitive elements that might accumulate errors during PCR amplification to produce amplicon inserts.

Two experimental protocol approaches are described here for assembly of polynucleotides into a target nucleic acid. These are constant 37° C. single temperature incubations, or cycling protocols alternating between 37° C. (optimal temperature for endonuclease digestion within a temperature range for ligase stability), and 16° C. (optimal temperature for ligation). The assembly protocol suggestions were based on the number of inserts in the assembly reaction, but there is considerable flexibility; hence, the computer output provides the optimal experimental conditions for a set of overhangs with selected % ligation fidelity. In the present example:

-   -   (a) Assembly of 1-4 inserts did not use cycling; and ligation         was achieved at a single temperature of 37° C.     -   (b) Multiple inserts used cycling assemblies with 1-minute         temperature steps.     -   (c) Cycling assemblies using 5-10-minute temperature steps was         also used for larger scale assemblies (>10 inserts) to provide         maximal assembly yields and transformation levels.     -   (d) For convenience, overnight incubations with 30 cycles of 37°         C., 5 minutes 16° C., 10 minutes, followed by 60° C., 5 minutes         and then 4° C. were also used. This resulted in high levels of         accurate assemblies with low background (for 24 fragment         assemblies). Bsal-HFv2 and T4 DNA Ligase however are very         stable, and they will continue to function at least up to 60         cycles and beyond.         Multiplex PCR: One-Pot PCR Generation of fragments for assembly

Gene fragments flanked by selected restriction endonuclease cut sites were individually precloned into pUC57-mini plasmids with any internal restriction sites in the amp^(R) gene removed through silent mutagenesis. The resulting plasmids (10 ng each) were amplified simultaneously in a single PCR reaction using 1×Q5® Hot Start PCR Master Mix (New England Biolabs, Ipswich, Mass.) and a common set of two amplification primers (100 uM each). Amplified fragments were then purified using a Monarch® DNA cleanup kit (New England Biolabs, Ipswich, Mass.) and quantified by capillary electrophoresis using an Agilent Bioanalzyer.

The PCR-amplified fragments (230 ng) were then combined with 1 μL of T4 DNA ligase buffer containing wt T4 DNA ligase (1000 u) and BsaHFv2 restriction endonuclease (30 U) for 5 hours and drop-down cycled between 37° C. and 16° C. Final assembly products were then transformed into chemically competent E. coli, plated, and yield, fidelity and efficiency were quantified as described in Table 8.

An Example of a Workflow for Generating an Ordered Assembly of Polynucleotides into a Target Polynucleotide

A workflow could be largely or entirely accomplished in a single machine with various component inputs presented together or sequentially. In a hypothetical workflow, a desired sequence is entered into the computer. The computer then provides an output describing the suitable fragments, and overhangs derived from the ligation frequency table to which sets of rules have been attached for ordered assembly of the desired sequence.

The computer output might interface with a lab on a chip or other instrument containing multiple reagent compartments. The regulation of reaction steps may be controlled on a chip by electrowetting based liquid transfer. For example, AQdrop® platform (Sharp Life Sciences, Oxford, UK) enables micro-scale droplets to be electronically manipulated on the “lab-on-a-chip” device. Another platform is an acoustic based-liquid transfer (Beckman Coulter, Brea, Calif.). Alternatively, the workflow may be performed using magnetic beads to remove unwanted enzymes/primers from a reaction vessel at different stages as needed.

Accordingly, fragments may be synthesized in situ or from a secondary source according to the computer output. The synthesized fragments can be amplified by cloning or by an amplification method such as PCR. The latter may be achieved by combining all the separate synthesized fragments in a single mixture and performing multiplex PCR. The polymerase may be inactivated, and a ligase and a restriction endonuclease added to achieve ordered DNA assembly using the methods described herein. The subsequent assembled target DNA may be (i) incorporated into a vector that in turn is introduced into a host cell by transformation of the vector; (ii) encapsulated into a virus and introduced into a host cell by infection; (iii) in the form of naked DNA or with a chaperone molecule, introduced directly into a eukaryotic cell; (iv) introduced into an in vitro expression system to determine whether the transcript of the assembled DNA is functional. Optionally, a product of the assembly could be moved to a platform location to perform sequencing such as by means of a whole molecule sequencer (Oxford Nanopore or Pacific Biosystems).

Ordered assembly of DNA molecules using the methods described herein, is a powerful tool for synthesizing individual genes or metabolic pathways and also for potentially modifying eukaryotic cells genetically. It also provides a means for synthesizing toxic proteins such as novel nucleases, to determine their specificity and other functions. Ordered assemblies encoding toxic proteins may be transcribed using an in vitro transcription system (New England Biolabs, Ipswich, Mass.) and then tested for DNA cleavage to determine whether a desired function is achieved. The selected positive proteins can then be manufactured in cells under specialized conditions.

In one example of an automated workflow where a large molecule is built from small fragments, a first step would be to synthesize a set of fragments of at least 20 bases in length enzymatically (e.g., using a terminal transferase) or by chemical synthesis or as a product of PCR from a larger substrate or a set of overlapping fragments.

These fragments can be assembled using the protocols described herein. An assembly of 50 fragments of 25-bases would generate a target polynucleotide of 1000 bases. The restriction endonuclease and ligase can optionally be heat killed at 60° C. prior to the next assembly step.

The assembly process may be repeated again with the newly created polynucleotide fragments. For example, primers, aptamers and polymerases for amplifying newly formed polynucleotide fragments from the previous step can then be generated by multiplex PCR. Subsequently, the amplified polynucleotide fragments are subjected to restriction endonuclease cleavage and ligation to generate a 12,500 bp fragment from 50×250 bp polynucleotides or a 50,000 bp polynucleotide from 50×1000 bp fragments.

The assembly can then be repeated for example by combining 50×12,500 (625 Kb) fragments or the 50×50,000 bp fragments (2.5 Mb), followed by cleavage and ligation to generate a 625 kb or 2.5 Mb target polynucleotide.

Another example of a workflow would be a one-step DNA assembly using a large number of DNA fragments of a size ranging from 200-1000 bp.

The efficiency of ligation of fragments depends on the overhangs, enzymes and experimental conditions but does not depend on the length of the polynucleotide fragments used in assembly at least up to 1 kb. The assembly of large number of fragments used in the assembly beyond 24 fragments may be preferentially accomplished by extended incubation periods. Where these incubation periods exceed 24 hours, it may be preferable to use a static ligation protocol instead of touch-down or drop-down protocol. The wt T4 ligase may be used in thermocycling up to temperatures defined by drop-down conditions of 42° C./16° C. Above 42° C., a thermostable ligase is preferable.

Proposed Uses of the Workflow Described Herein

One tube, multiple constructs: emulsified ordered assembly workflow could enable users to generate different constructs from multiple fragment in a small droplet-based format where “positive” drops can be sorted for downstream applications by FACS. Mismatch connections during ordered assembly could enable users to generate different variations of constructs in one tube by the purposeful use of an overhang(s) that pair well with multiple partners. For example, a user could generate the same genetic circuit with several different promoters in one tube and identify the best construct through genetic screening.

Assembly of higher order DNA structures (using non-standard DNA parts). DNA Origami could enable users to assemble DNA structures to facilitate transfection and consistent genetic regulation by controlling shape of assembled molecule. Branched Construct Generation could enable users to create futuristic constructs with branched configurations for parallel regulation. For example, use of a non-standard part assembly fragments (1 duplex to 2 duplex connectors etc.) could position to coding sequence close to the same insulator element.

Mixed overhang length for ordered assembly resulting from the use of more than one Type IIS enzyme could enable maximizing fragments numbers for assembly and permit users to increase the numbers of overhangs possible in a single reaction by mixing orthogonal sets of overhangs with different lengths. This approach could also generate a final construct with a bubble to facilitate downstream applications (including strand invasion or cleavage of the product by nucleases (e.g., T7 endo I)).

Having now described an example embodiment, it should be apparent to those skilled in the art that the foregoing is merely illustrative and not limiting, having been presented by way of example only. Numerous modifications and other embodiments are within the scope of one of ordinary skill in the art and are contemplated as falling within the scope of the invention.

TABLE 8 Temps Fidelity Test System Cycling ° C. Ligase Type IIS Overhang Time Additive Yield % Efficiency [Protein] Touch-down Cycling increases assembly fidelity and reduces background colonies >2-fold 12-Fragment Drop-down 37/16 wt T4 BsaI-HFv2 4bp 5 hr No 3760 55 752  500/15 Touch-up* 37/16 wt T4 BsaI-HFv2 4bp 5 hr No 2860 51 572  500/15 Touch-down 37/16 wt T4 BsaI-HFv2 4bp 5 hr No 2660 76 532  500/15 Touch-down cycling increases assembly fidelity over drop-down cycling 2-Fragment Drop-down 37/16 wt T4 BsaIHFv2 4bp 5 hr No 43.18 58 8.6 2000/15 Touch-down 37/16 wt T4 BsaIHFv2 4bp 5 hr No 48.43 77 9.7 2000/15 High temp touch-down increases assembly fidelity compared to a lower temperature touch-down protocol 12-Fragment Touch-down 37/16 Hi-T4 BsaIHFv2 4bp 5 hr No 5600 64 1120  500/15 Touch-down 45/16 Hi-T4 BsaIHFv2 4bp 5 hr No 4520 74 904  500/15 Salt increases assembly yield >2-fold in the optimized concentration range 24-Fragment Drop-down 42/16 wt T4 BsmBI 4bp 5 hr No 51 55 10 1000/30 Drop-down 42/16 wt T4 BsmBI 4bp 5 hr Salt 2.5  8 1 1000/30 (100 mM) Drop-down 42/16 Salt-T4 BsmBI 4bp 5 hr Salt 148 66 30 1000/30 Ligase (100 mM) High Temperature increases assembly yield and accuracy using BsmBI 24-Fragment Drop-down 37/16 wt T4 BsaI-HFv2 4bp 5 hr No 114 88 23 1000/30 Drop-down 37/16 wt T4 BsmBI 4bp 5 hr No 1 15 0 1000/30 Drop-down 40/16 wt T4 BsmBI 4bp 5 hr No 7 18 1 1000/30 Drop-down 42/16 wt T4 BsmBI 4bp 5 hr No 56 48 11 1000/30 Drop-down 45/16 wt T4 BsmBI 4bp 5 hr No 2 27 0 1000/30 Drop-down 47/16 wt T4 BsmBI 4bp 5 hr No 0 N/A 0 1000/30 Drop-down 50/16 wt T4 BsmBI 4bp 5 hr No 0 N/A 0 1000/30 Drop-down 37/16 Hi-T4 BsmBI 4bp 5 hr No 0 N/A 0 1000/30 Drop-down 40/16 Hi-T4 BsmBI 4bp 5 hr No 6 11 1 1000/30 Drop-down 42/16 Hi-T4 BsmBI 4bp 5 hr No 40 44 8 1000/30 Drop-down 45/16 Hi-T4 BsmBI 4bp 5 hr No 182 70 36 1000/30 Drop-down 47/16 Hi-T4 BsmBI 4bp 5 hr No 282 82 56 1000/30 Drop-down 50/16 Hi-T4 BsmBI 4bp 5 hr No 380 88 76 1000/30 52-fragments (4bp overhangs) are assembled in one-pot using a high temp touch-down protocol (lac cassette) Temps Test System Cycling ° C. Ligase Type IIS Overhang Time Additive Yield Fidelity Efficiency [Protein] 52-Fragment Touch-down 50/16 wt T4 BsaI-HF 4bp 24 hr No 0 N/A N/A 1000/30 Touch-down 50/16 Hi-T4 BsaI-HF 4bp 24 hr No 1.1 N/A 2.2 1000/30 Temps Fidelity Test System Cycling ° C. Ligase Type IIS Overhang Time Additive Yield % Efficiency [Protein] T7 Phage genome assembled from 10-fragments (3-base overhang) in one-pot using a high temp digestion protocol 10-Fragment Drop-down 50/16 wt T4 BspQI 3bp 16 hr No 0 N/A 0  500/15 Drop-down 50/16 Hi-T4 BspQI 3bp 16 hr No 1768 N/A 110.5  500/15 T7 Phage genome assembled from 52 fragments (4-base overhang) in one-pot using a high temp drop-down cycling 52-Fragment Drop-down 42/16 wt T4 BsmBI 4bp  5 hr No 11 N/A 2.2 1000/30 Drop-down 42/16 Wt T4 BsmBI 4bp 16 hr No 141 N/A 8.8 1000/30 Assembly at high temperatures with BsaI-HFv2 Temps Fidelity Test System Cycling ° C. Ligase Type IIS Overhang Time Additive Yield* % Efficiency [Protein] 2-Fragment Static 37 wt T4 BsaI-HFv2 4bp 16 hr No 38.3 83 2.39 2000/15 Static 45 wt T4 BsaI-HFv2 4bp 16 hr No 0 N/A 0 2000/15 Static 50 wt T4 BsaI-HFv2 4bp 16 hr No 0 N/A 0 2000/15 Static 37 Hi-T4 BsaI-HFv2 4bp 16 hr No 36.6 81 2.29 2000/15 Static 45 Hi-T4 BsaI-HFv2 4bp 16 hr No 25.9 93 1.62 2000/15 Static 50 Hi-T4 BsaI-HFv2 4bp 16 hr No 14 96 0.87 2000/15 Assembly at high temperatures (thermostable BspQI) increases assembly accuracy Temps Accuracy Test System Cycling ° C. Ligase Type IIS Overhang Time Additive Yield* % Efficiency [Protein] 2-Fragment Static 37 wt T4 BspQI 3bp 16 hr No 38 95 2.38 500/15 Static 45 wt T4 BspQI 3bp 16 hr No 0 N/A 0 500/15 Static 50 wt T4 BspQI 3bp 16 hr No 0 N/A 0 500/15 Static 37 Hi-T4 BspQI 3bp 16 hr No 40.85 95 2.55 500/15 Static 45 Hi-T4 BspQI 3bp 16 hr No 38.8 97 2.43 500/15 Static 50 Hi-T4 BspQI 3bp 16 hr No 11.96 98 0.75 500/15 Temps Fidelity Test System Cycling ° C. Ligase Type IIS Overhang Time Additive Yield % Efficiency [Protein] Multiplex PCR - Decreases time/effort required to generate assembly parts: Demonstrates Successful 24-Fragment Assembly from One-Pot PCR Method 24-Fragment Drop-down 37/16 wt T4 BsaI-HFv2 4bp 5 hr No 9.2 92 2 1000/30  12-Fragment Assembly from One-Pot PCR Method 12-Fragment Drop-down 37/16 wt T4 BsaI-HFv2 4bp 5 hr No 792 97 158 500/15 EndoMS Cleanup - Increases assembly fidelity: EndoMS reduces background colonies >2-fold 12-Fragment Drop-down 37/16 wt T4 BsaI-HFv2 4bp 5 hr No 3260 59 652 500/15 Drop-down 37/16 wt T4 BsaI-HFv2 4bp 5 hr EndoMS 3090 84 618 500/15 EndoMS reduces background colonies >2-fold 12-Fragment Drop-down 37/16 wt T4 BsaI-HFv2 4bp 5 hr No 7075 45 1415 500/15 Drop-down 37/16 wt T4 BsaI-HFv2 4bp 5 hr EndoMS 7150 70 1430 500/15 EndoMS treatment improves fidelity of touch-down cycling assembly protocol 12-Fragment Touch-down 37/16 wt T4 BsaIHFv2 4bp 5 hr No 270 68 54 500/15 Touch-down 37/16 wt T4 BsaIHFv2 4bp 5 hr EndoMS 810 89 162 500/15 Temps Accuracy Test System Cycling ° C. Ligase Type IIS Overhang Time Additive Yield* % [Protein] EndoMS treatment increases assembly accuracy 2-Fragment Drop-down 37/16 wt T4 BsaI-HFv2 4bp 5 hr No N/A 58 2000/15 Drop-down 37/16 wt T4 BsaI-HFv2 4bp 5 hr EndoMS N/A 72 2000/15 EndoMS treatment increases assembly accuracy 2-Fragment Drop-down 37/16 wt T4 SapI 3bp 5 hr No N/A 88 1000/15 Drop-down 37/16 wt T4 SapI 3bp 5 hr EndoMS N/A 95 1000/15 Yield—Total amount of positive assemblies or plaques. For the 2-fragment assembly, yield is ng product. Fidelity—Yield/total assemblies or product (blue colonies/white colonies) Efficiency—Yield/hour [Protein]—Ligase concentration (units) and Type IIS concentration (units)/20 μl reaction Accuracy—Number of correct end joining of fragments over number of total assemblies Hi-T4—Thermostable T4 DNA ligase variant Salt-T4—Salt tolerant T4 DNA ligase variant EndoMS was used at a concentration of 3.4 μg/20 μl reaction

Example 6: Rapid One-Pot DNA Molecule Construction from 50 Fragments of 40 Kb T7 Phage DNA and from 52 Fragments of the 4.9 Kb Lac Operon with High Fidelity

Enzymes, buffers, and media were obtained from New England Biolabs, Ipswich, Mass. (NEB), unless otherwise noted. Synthetic oligonucleotides were obtained from either Integrated DNA Technologies (IDT) or Sigma Aldrich (Sigma).

DNA Sequencing Assay

Substrates for the DNA sequencing assay were prepared as previously described. Golden Gate assembly reactions (20 μL final volume) to generate sequencing libraries were carried out in 1×T4 DNA ligase buffer by combining: 100 nM of DNA substrate (final concentration) with 2 μL of NEB Golden Gate Enzyme Mix (Bsal-H Fv2 or BsmBl-v2). Reactions were carried out for 16 hours at 37° C. (Bsal-HFv2) or 42° C. (BsmBl-v2). Reactions were then quenched by the addition of 25 mM EDTA and column purified (Monarch PCR & DNA Cleanup Kit). The resulting assembly products were further purified to remove un-ligated substrate by treatment with Exonuclease III (50 U) and Exonuclease VII (5 U) in 1× Standard Taq Polymerase buffer (final concentration) for 1 hour at 37° C. in a 50 μL reaction volume. The assembly products were then re-purified using the Monarch PCR & DNA Cleanup Kit and quantified by Agilent Bioanalyzer (DNA 1000).

Pacific Biosciences Single-Molecule Real-Time (SM RT) sequencing was performed as described previously. The libraries were prepared for sequencing using the PacBio Binding Calculator Version 2.3.1.1 and the DNA/Polymerase Binding Kit P6 v2 with a custom library concentration on the plate of 0.3375 nM. Sequencing was carried out using the PacBio RSII instrument with at least 2 SMRT cells per library and a 3 hour data collection time per cell with ‘stage start’ off. Consensus sequences for each assembly product were generated as described previously. Full results from each experiment are supplied in the supporting data files (S1-S2 Tables).

Golden Gate Assembly Reactions

Assembly fragments were generated by PCR (Q5 hot-start high-fidelity 2× master mix) with oligonucleotide primers (IDT) and purified using the Monarch PCR & DNA Cleanup Kit. Fragment quality was evaluated using the Agilent Bioanalyzer 2100 and each assembly part was quantified using the Qubit assay (Thermo Fisher Scientific, Waltham, Mass.). Golden Gate assembly reactions (5 μL final volume) were carried out with 3 nM of each DNA fragment and 0.5 μL of the appropriate NEB Golden Gate Assembly Mix in 1× T4 DNA ligase buffer; the Bsal-HFv2 mix was used to reconstitute the lac operon cassette and the BsmBl-v2 mix was used to assemble the T7 phage genome. Reactions to reconstitute the lac operon cassette were incubated for 48 hours at 37° C. and then subjected to a final heat-soak step at 60° C. for 5 minutes before being incubated at 4° C. prior to transformation. Reactions to produce the T7 bacteriophage genome were cycled between 42° C. and 16° C. for 5 minutes at each temperature for 96 cycles, and then subjected to a 60° C. incubation for 5 minutes and finally a 4° C. hold until transformation.

Clonogenic Assays

Assembly reactions to reconstruct the lac operon cassette were transformed into chemically competent E. coli cells, and colony forming units were scored as harboring correctly or erroneously assembled constructs by a reverse blue-white screen as described previously. Briefly, transformations were performed using 2 μL of each assembly reaction added to 50 μL of T7 express competent cells as per manufacturer's instructions. The resulting outgrowth was plated onto agar plates (Luria-Bertani broth supplemented with 1 mg/mL dextrose, 1 mg/mL MgCl2, 30 μg/mL Chloramphenicol, 200 μM IPTG and 80 μg/mL X-gal). Importantly, transformants harboring correctly assembled constructs turn blue after incubation on media containing IPTG and X-Gal, while transformants harboring constructs with assembly errors form white colonies.

Plaque Assays

Reactions to construct the T7 phage genome were transformed into NEB 10-beta cells as per the manufacturer's instructions, using 1 μL of the reaction mixture into 25 μL of competent cells. The transfection mixture was recovered in 975 μL of NEB 10-beta/stable outgrowth media and then combined with 3 mL of 50° C. molten top-agar (Luria broth containing 0.7% agar). Finally, the mixture was plated on LB agar plates and the molten agar was allowed to cool and solidify on the benchtop for 20 m. The resulting pates were inverted and incubated at 37° C. for ^(˜)5 h until the E. coli lawn and phage plaques were visible by eye.

The impact of reaction temperature on Golden Gate assembly fidelity

Golden Gate assembly typically utilizes two step cycling protocols, alternating between a 16° C. incubation step to maximize DNA ligation efficiency and a 37-42° C. incubation step to maximize fragment digestion efficiency. The omission of 16° C. incubation was tested to determine the effect on Golden Gate assembly fidelity, as higher reaction temperatures have been shown to improve DNA ligase fidelity. The frequency of Golden Gate assembly errors at 37° C. or 42° C. was quantified in a multiplex high throughput DNA sequencing assay, and the results compared to reactions using traditional thermocycling protocols of 37/16° C. or 42/16° C. The reactions carried out at constant incubation temperatures were incubated for an extended duration, 16 hours, to compensate for decreased ligation efficiency. The results showed that the frequency of ligation errors was diminished>2-fold when the 16° C. incubation step was omitted, with every mismatch pair appearing less frequently.

We found that the capacity of Golden Gate assembly reactions could exceed 50 fragments per reaction using a single temperature incubation (static). In this example using Bsal or BsmBl restriction endonuclease, the estimated assembly fidelity for traditional 37/16° C. or 42/16° C. cycling conditions dropped below 10% at 50 fragments, but the 37° C. or 42° C. static incubation protocols could allow>50 fragment to be assembled with >40% accuracy. The static 37° C. or 42° C. static temperature utilized longer incubation times to compensate for the efficiency loss caused by omitting the 16° C. incubation step.

Mismatch frequencies for assembly reactions were grouped according to nucleotide mispair (A:A, A:C, A:G, C:C, C:T, G:G, G:T, T:T). Assembly reactions were carried out with T4 DNA ligase and either Bsal-HFv2 at 37° C. or BsmBl-v2 at 42° C. For comparison, mismatch frequencies are shown for assembly reactions using traditional thermocycling protocols with T4 DNA ligase and either Bsal-HFv2 at 37° C. and 16° C. or BsmBl-v2 at 42° C. and 16° C. Mismatch frequency was significantly lower using Bsal-HF-v2 (37° C.) or BsmBl-v2 (42° C.) at a single temperature than observed for cycling.

Verification of the 52 Fragment Lac Operon Cassette Assembly

Plasmid DNA was isolated from 18 blue colonies using the Monarch Plasmid Miniprep kit (New England Biolabs, Ipswich, Mass.). Twelve of the resulting constructs were subjected to PCR with amplification primers that flank the desired insertion site. Every construct yielded an amplicon size consistent with assembly of all 52 fragments, demonstrating that blue colonies contained the desired number of inserts. Six of the isolated constructs were sequenced using nine different sequencing primers to cover the entire 4.9 kb expected insert. All 6 constructs contained ordered error-free assembly of all 52-inserts.

Verification of 50 Fragment T7 Phage gDNA Assembly

Plaque PCR was carried out using 4 sets of amplification primers (A-D) that together span the 38 kb phage genome. Amplicon lengths were resolved by Agilent Bioanalzyer 2100, using a DNA 10000 assay. Amplicons from 5 phage plaques were compared to the parental T7 phage genome after restriction enzyme digest with Ndel or undigested. In all cases, the phage plaques produced a pattern identical to the parental T7 genome DNA. To confirm that the assembled genome harbored the desired silent mutations that remove native BsmBl restriction sites and verify that the observed plaques were not the results of carryover-contamination from the parental T7 phage gDNA, we also carried out amplicon digestion of the parental T7 phage genome and plaques with BsmBl. We showed that an amplicon from the parental T7 phage genome is digested by BsmBl to produce the bands of expected size, whereas the amplicons from the assembled phage genomes were inert to cleavage by BsmBl.

To test the predictions made herein, we carried out the most complex assembly reaction to-date and cloned a 4.9 kb cassette of the lac operon into an E. coli destination vector from 52 constituent parts in a single assembly round. Importantly, the lac operon cassette system used here mimics a traditional cloning reactions wherein, upon transformation of the assembly reaction into E. coli cells, we can observe colonies harboring correctly or incorrectly assembled constructs. This test system provides a colorimetric readout to differentiate transformants harboring correctly and incorrectly assembled products. We found that 49% of the observed transformants harbored correctly assembled constructs, in close agreement with our predicted fidelity of 40% (FIG. 21A-21B). To further confirm successful assembly of all 52 inserts, we purified constructs from a subset of colonies and analyzed the inserts by PCR and Sanger sequencing; all colonies subjected to additional screening were found to harbor constructs with inserts of the anticipated size and sequence.

Next, to test assembly of large targets in a single round from many small fragments, we designed a GGA reaction to construct the 38 kb T7 bacteriophage genome from 50 parts. As the phage genome contains many genes that are toxic to E. coli cells, we reconstructed the phage gDNA from PCR-generated DNA fragments to avoid subcloning toxic genes. Moreover, this strategy enabled us to easily introduce 16 silent mutations in the phage genome to remove pre-existing BsmBl Type IIS restriction sites within the genome. These changes serve dual purpose to both permit Type IIS assembly, and to act as marker mutations for assembly verification. Assembly reactions were carried out and transformed into NEB 10-beta electrocompetent cells; successful assembly of the T7 phage genome was assessed by plaque forming assay. Bacteriophage plaques were observed upon electroporation of the genome assembly reactions into E. coli cells, indicating successful assembly of the phage genome (FIG. 20A-20B). Several phage plaques were selected for additional screening by plaque PCR and restriction enzyme digest to ensure they contained a complete and properly ordered copy of the T7 phage genome; all plaques subjected to additional screening contained the expected genome arrangement and harbored the intended silent mutations. Moreover, to ensure the observed phage plaques were the result of in vitro assembly and not assembly of the DNA fragments within the E. coli by cellular DNA repair mechanisms, we carried out control reactions lacking T4 DNA ligase and did not observe phage plaques upon transformation of these control reactions. Of note, we found that the high-temperature assembly protocol variations were not necessary to produce infectious phage plaques; presumably due to the more stringent selection of the plaque forming assay, as improperly assembled variants of the T7 phage genome are unlikely to produce viable phage and thus there is no background from incorrectly assembled products as in the lac operon cassette test system. Taken together, these results demonstrate rapid assembly of a phage genome, and suggest that the methods developed here could be applied to other large and/or complex DNA targets.

In summary, our work demonstrates an efficient and cost-effective means to create and engineer variants of large/complex DNA constructs that are difficult to obtain and manipulate by current cloning and gene synthesis methodologies. Our results show that GGA could be used to rapidly assemble toxic and/or high molecular weight DNA constructs from dozens of smaller constituent parts that are easily manipulated and propagated using standard molecular biology techniques. These findings dramatically reduce the number of hierarchical assembly rounds required to produce large constructs by in vitro assembly and can be utilized to assemble entire metabolic pathways and even small genomes in a single reaction.

Example 7: Aprataxin/5′Deadenylase and PEG in Golden Gate Assembly

In reactions described in the Tables below as specified, ordered assembly reactions consisted of precloned DNA fragments (3 nM each) or PCR fragments (3 nM each) and the indicated amount of restriction enzyme and ligase in T4 DNA ligase buffer or Blunt T/A ligase buffer (New England Biolabs, Ipswich, Mass.). Assembly reactions were incubated as described in Example 3, using one of the three different ligation protocols, followed by a 5 minute final incubation step at 60° C. then a final 4° C. hold prior to transformation. Transformations were performed using 2 μl of each assembly reaction added to 50 μl competent T7 Express chemically competent E. coli (New England Biolabs, Ipswich, Mass.) plated on the appropriate growth media, and incubated at 37° C. to form colonies.

The correctly assembled target polynucleotides coded for a cassette of the lac operon (about 5 kb) so that blue colonies of correctly assembled fragments could be distinguished from white colonies containing incorrect assemblies on IPTG/Xgal/Chloramphenicol plates.

Generally, it was found that the addition of a 5′ Deadenylase enzyme or PEG 600-6000 increased the yield of correct assemblies.

Test System Cycling Temps Ligase Type IIS Overhang Time Additive Yield Efficiency [Protein] 5′ Deadenylase increases assembly yield >2-fold in the optimized concentration range (dropdown cycling) 24-Fragment Drop-down 37/16 wt T4 BsaI-HFv2 4bp  5 hr No 60 12 1000/30 Drop-down 37/16 wt T4 BsaI-HFv2 4bp  5 hr 5′De-ad 87 17.4 1000/30 (1.5 U) Drop-down 37/16 wt T4 BsaI-HFv2 4bp  5 hr 5′De-ad 109 21.8 1000/30 (5 U) Drop-down 37/16 wt T4 BsaI-HFv2 4bp  5 hr 5′De-ad 154 30.8 1000/30 (25 U) 5′Deadenylase increases assembly yield ~7-10-fold (Static cycling) 24-Fragment Static 37 wt T4 BsaI-HFv2 4bp 24 hr No 12 0.5 1000/30 Static 37 wt T4 BsaI-HFv2 4bp 24 hr 5′De-ad 94 3.91 1000/30 (25 U) Static 42 Hi T4 BsaI-HFv2 4bp 24 hr No 2 0.08 1000/30 Static 42 Hi T4 BsaI-HFv2 4bp 24 hr 5′De-ad 20 0.83 1000/30 (25 U) 5′ Deadenylase increases assembly yield >3-fold (Touch-down cycling) 52-Fragment Touch-down 50/16 Hi T4 BsaI-HFv2 4bp 24 hr No 1.1 0.05 1000/30 Touch-down 50/16 Hi T4 BsaI-HFv2 4bp 24 hr 5′De-ad 4.3 0.18 1000/30 (25 U) PEG 600-6000 increases assembly yield ~2-5-fold 24-Fragment Drop-down 37/16 wt T4 BbsI-HF 4bp 10 hr No 296 29.6 1000/60 Drop-down 37/16 wt T4 BbsI-HF 4bp 10 hr PEG 600 557 55.7 1000/60 (6.8%) Drop-down 37/16 wt T4 BbsI-HF 4bp 10 hr PEG 3350 1421 142.1 1000/60 (6.8%) Drop-down 37/16 wt T4 BbsI-HF 4bp 10 hr PEG 6000 1157 115.7 1000/60 (6.8%) Ratio of T4 ligase to BbsI-HF impacts assembly yield 24-Fragment Drop-down 37/16 wt T4 BbsI-HF 4bp 10 hr No 425 4.25  400/60 Drop-down 37/16 wt T4 BbsI-HF 4bp 10 hr No 1120 112 1000/60 Drop-down 37/16 wt T4 BbsI-HF 4bp 10 hr No 1130 113 2000/60 Yield—Total amount of positive assemblies or plaques. Fidelity—Yield/total assemblies or product (blue colonies/white colonies) Efficiency—Yield/hour [Protein]—Ligase concentration (units) and Type IIS concentration (units)/20 μl reaction Accuracy—Number of correct end joining of fragments over number of total assemblies Hi-T4—Thermostable T4 DNA ligase variant 5′ De-ad—5′ Deadenylase and protein concentration in units (U)

Example 8: Synthesis and Engineering of a Viral Genome for Research and Vaccine Development

Reverse genetic systems that rely on in vitro ligation offer researchers a relatively fast/efficient way to generate variants of RNA viruses for research purposes and vaccine development efforts. This methodology has worked for manipulation of several viruses but has not yet been successfully applied to many high-value targets, including coronaviruses (despite several attempts). It is likely that the large size and inherently toxic/repetitive nature of some viral genomes prohibits maintenance of the viral genomic DNA in E. coli cells by traditional techniques. However, efficient assembly of the viral genome from many parts can be accomplished using the methods described herein. Toxic viral genomes can be sub-divided into small fragments for easy manipulation in E. coli cells, permitting one-tube assembly of the viral cDNA in a few hours. As an example, we demonstrate below the designs of a 12-fragment, 24-fragment, and 50-fragment linear viral genome assembly (Genbank ID: NC_045512, from severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1,complete genome).

5′ Fragment # Range Length End 3′End Segments of a 12-Fragment viral genome (Genbank ID: NC_045512) 1   1-2501 2531 bp  AGTG 2 2502-4993 2522 bp  CACT TAAT 3 4994-7479 2516 bp  ATTA TGAA 4 7480-9967 2518 bp  TTCA TTGC 4  9968-12468 2531 bp  GCAA TTTG 5 12469-14945 2507 bp  CAAA ACCA 6 14946-17436 2521 bp  TGGT GGTC 7 17437-19926 2520 bp  GACC TAGA 8 19927-22437 2541 bp  TCTA AAGT 9 22438-24912 2505 bp  ACTT GTCT 11 24913-27405 2523 bp  AGAC AAAG 12 27406-29903 2528 bp  CTTT Segments of a 24-Fragment viral genome (Genbank ID: NC_045512) 1   1-1245 1275 bp  TTCA 2 1246-2500 1285 bp  TGAA GTGT 3 2501-3735 1265 bp  ACAC AGGG 4 3736-4985 1280 bp  CCCT TCTA 5 4986-6234 1279 bp  TAGA AACA 6 6235-7470 1266 bp  TGTT ACCG 7 7471-8729 1289 bp  CGGT GTAG 8 8730-9964 1265 bp  CTAC CGAG 9  9965-11220 1286 bp  CTCG GACC 10 11221-12468 1278 bp  GGTC TTTG 11 12469-13713 1275 bp  CAAA AATC 12 13714-14949 1266 bp  GATT GAAA 13 14950-16201 1282 bp  TTTC TCAT 14 16202-17451 1280 bp  ATGA CAGG 15 17452-18690 1269 bp  CCTG TGGA 16 18691-19939 1279 bp  TCCA GCTA 17 19940-21190 1281 bp  TAGC TCAG 18 21191-22437 1277 bp  CTGA AAGT 19 22438-23680 1273 bp  ACTT AGTA 20 23681-24921 1271 bp  TACT AAAT 21 24922-26157 1266 bp  ATTT TAAC 22 26158-27405 1278 bp  GTTA AAAG 23 27406-28649 1274 bp  CTTT TTGT 24 28650-29903 1284 bp  ACAA Segments of a 50-Fragment viral genome (Genbank ID: NC_045512) 1  1-595 625 bp CCAC 2  596-1194 629 bp GTGG TTCA 3 1195-1784 620 bp TGAA TTAC 4 1785-2395 641 bp GTAA GCGT 5 2396-2996 631 bp ACGC CCAG 6 2997-3594 628 bp CTGG AGCA 7 3595-4189 625 bp TGCT TAGT 8 4190-4792 633 bp ACTA AGGA 9 4793-5387 625 bp TCCT TTAG 10 5388-5989 632 bp CTAA GCTC 11 5990-6579 620 bp GAGC AGTA 12 6580-7170 621 bp TACT AGAA 13 7171-7781 641 bp TTCT TTAT 14 7782-8366 615 bp ATAA TGCG 15 8367-8965 629 bp CGCA GTTT 16 8966-9561 626 bp AAAC GAAT 17  9562-10166 635 bp ATTC GGAC 18 10167-10759 623 bp GTCC ACTT 19 10760-11364 635 bp AAGT ATAC 20 11365-11968 634 bp GTAT CTTT 21 11969-12557 619 bp AAAG TGGA 22 12558-13159 632 bp TCCA TACA 23 13160-13754 625 bp TGTA TATT 24 13755-14351 627 bp AATA TCTG 25 14352-14946 625 bp CAGA AACC 26 14947-15539 623 bp GGTT CGTG 27 15540-16154 645 bp CACG CATA 28 16155-16749 625 bp TATG TAGG 29 16750-17343 624 bp CCTA CTAT 30 17344-17937 624 bp ATAG TTGC 31 17938-18543 636 bp GCAA ACAT 32 18544-19129 616 bp ATGT TCTT 33 19130-19743 644 bp AAGA ACAA 34 19744-20324 611 bp TTGT AACG 35 20325-20936 642 bp CGTT CAGC 36 20937-21526 620 bp GCTG GAAA 37 21527-22131 635 bp TTTC TTCC 38 22132-22724 623 bp GGAA TCAT 39 22725-23320 626 bp ATGA TAAT 40 23321-23915 625 bp ATTA TTGA 41 23916-24514 629 bp TCAA TGTC 42 24515-25117 633 bp GACA TGAG 43 25118-25706 619 bp CTCA GAGA 44 25707-26310 634 bp TCTC CGAA 45 26311-26909 629 bp TTCG TGGT 46 26910-27511 632 bp ACCA TCGT 47 27512-28115 634 bp ACGA TATC 48 28116-28703 618 bp GATA TGAT 49 28704-29303 630 bp ATCA TTTG 50 29304-29903 630 bp CAAA 

What is claimed is:
 1. A synthetic self-complementary oligonucleotide that comprises a double-stranded region and a loop, wherein the double-stranded region contains a binding sequence for PaqCl and wherein the oligonucleotide and comprises unligatable 3′ and 5′ end and cannot be cleaved by PaqCl.
 2. The oligonucleotide of claim 1, wherein the double-stranded region is 10-50 base pairs in length.
 3. The oligonucleotide of claim 1, wherein the oligonucleotide is less than 110 nucleotides in length.
 4. The oligonucleotide of claim 1, wherein the 3′ end of the oligonucleotide is not a 3′ hydroxyl.
 5. The oligonucleotide of claim 1, wherein the 5′ end of the oligonucleotide is not a 5′ phosphate.
 6. The oligonucleotide of claim 1, wherein the binding sequence is CACCTGC.
 7. A reaction mixture, comprising: (a) a synthetic self-complementary oligonucleotide of claim 1; and (b) PaqCl or a variant thereof having an amino acid sequence that has at least 90% amino acid sequence identity with SEQ ID NO:26.
 8. The reaction mixture of claim 7, further comprising a double-stranded DNA substrate for PaqCl, wherein the substrate contains a binding sequence for PaqCl and can be cleaved by PaqCl to produce a 4-base overhang.
 9. The reaction mixture according to claim 8, wherein the binding sequence in the DNA substrate is CACCTGC.
 10. The reaction mixture of claim 7, further comprising a ligase.
 11. The reaction mixture according to any of claim 7, further comprising a plurality of DNA substrates containing a binding site for PaqCl, wherein cleavage of the DNA substrates by PaqCl or variant thereof produces a plurality of fragments that have compatible overhangs that can be ligated into a single molecule.
 12. The reaction mixture of claim 11, wherein the reaction mixture comprises at least 20 DNA substrates containing the binding site for PaqCl.
 13. The reaction mixture of claim 11, wherein the ratio of the PaqCl or variant to ligase is 2.5-20 units PaqCl or variant to 200-800 units of ligase.
 14. A method comprising: (a) combining: i. a synthetic self-complementary oligonucleotide of claim 1; ii. PaqCl or a variant thereof having an amino acid sequence that has at least 90% amino acid sequence identity with SEQ ID NO:26; iii. a plurality of DNA substrates for PaqCl, wherein cleavage of the DNA substrates by PaqCl or variant thereof produces a plurality of fragments that have compatible overhangs that can be ligated into a single molecule; and iv. a ligase, to produce a reaction mix; and (b) incubating the reaction mix to produce a reaction product that comprises a DNA molecule that comprises sequence from the plurality of fragments.
 15. The method of claim 14, further comprising transforming cells with the reaction product.
 16. The method of claim 14, wherein the reaction mix in a(iv) further comprises at least one of a DNA repair enzyme, a deadenylase, a crowding agent and/or the incubating is done by thermocycling.
 17. The method of claim 16, wherein the reaction mix comprises polyethylene glycol (PEG) having a molecular weight in the range of 600-8000.
 18. The method of claim 16, wherein the deadenylase is a yeast deadenylase.
 19. The method of claim 16, wherein the DNA repair enzyme is EndoMS.
 20. The method according to claim 14, wherein the plurality of DNA substrates is 20-100 DNA substrates.
 21. The method according to claim 14, wherein the plurality of DNA substrates is at least 50 DNA substrates.
 22. A kit for use in synthesizing a DNA from component sequences that are either contained in oligonucleotide fragments, cDNA or in genomic DNA, wherein the kit comprises: a Type IIS restriction endonuclease having at least 90% sequence identity to SEQ ID NO:26, a ligase, and optionally an additive selected from the group consisting of a deadenylase and a crowding agent.
 23. The kit according to claim 22, wherein the Type IIS restriction endonuclease and the ligase are combined in a single container.
 24. The kit according to claim 22, wherein the Type IIS restriction endonuclease and the ligase are in separate containers.
 25. The kit according to claim 22, further comprises synthetic self-complementary oligonucleotide that comprises a double-stranded region and a loop, wherein the double-stranded region contains a binding sequence for PaqCl and wherein the oligonucleotide cannot be cleaved by PaqCl and comprises unligatable 3′ and 5′ ends.
 26. The kit according to claim 22, wherein the kit contains a deadenylase that has at least 90% sequence identity to any of SEQ ID NO:18-25.
 27. The kit according to claim 22, wherein the crowding agent is polyethylene glycol (PEG).
 28. The kit according to claim 22, wherein the PEG has a molecular weight in the range of 600-8000.
 29. The kit according to claim 22, wherein the kit further comprises a mismatch specific endonuclease.
 30. The kit according to claim 29, wherein the mismatch endonuclease is EndoMS.
 31. The kit according to claim 22, further comprising in the same or separate container, one or more destination vectors.
 32. The kit according to claim 22, wherein the kit further comprises competent prokaryotic or eukaryotic cells for receiving the destination vector. 